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1    # -*- perl -*-
2    ########################################################################
3    # Copyright (c) 2003-2006 University of Chicago and Fellowship
4    # for Interpretations of Genomes. All Rights Reserved.
5    #
6    # This file is part of the SEED Toolkit.
7    #
8    # The SEED Toolkit is free software. You can redistribute
9    # it and/or modify it under the terms of the SEED Toolkit
10    # Public License.
11    #
12    # You should have received a copy of the SEED Toolkit Public License
13    # along with this program; if not write to the University of Chicago
14    # at info@ci.uchicago.edu or the Fellowship for Interpretation of
15    # Genomes at veronika@thefig.info or download a copy from
16    # http://www.theseed.org/LICENSE.TXT.
17    ########################################################################
18    
19  package Tracer;  package Tracer;
20    
         require Exporter;  
         @ISA = ('Exporter');  
         @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert);  
         @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape);  
21          use strict;          use strict;
22          use Carp qw(longmess croak);      use base qw(Exporter);
23        use vars qw(@EXPORT @EXPORT_OK);
24        @EXPORT = qw(Trace T TSetup QTrace Confess Cluck Min Max Assert Open OpenDir TICK StandardSetup EmergencyKey ETracing Constrain Insure ChDir Emergency Warn TraceDump IDHASH);
25        @EXPORT_OK = qw(GetFile GetOptions Merge MergeOptions ParseCommand ParseRecord UnEscape Escape PrintLine PutLine);
26        use Carp qw(longmess croak carp);
27          use CGI;          use CGI;
28        use Cwd;
29          use FIG_Config;          use FIG_Config;
30      use PageBuilder;      use PageBuilder;
31        use Digest::MD5;
32        use File::Basename;
33        use File::Path;
34        use File::stat;
35        use LWP::UserAgent;
36        use Time::HiRes 'gettimeofday';
37        use URI::Escape;
38        use Time::Local;
39        use POSIX qw(strftime);
40        use Time::Zone;
41        use Fcntl qw(:DEFAULT :flock);
42        use Data::Dumper;
43    
44    
45  =head1 Tracing and Debugging Helpers  =head1 Tracing and Debugging Helpers
46    
47  =head2 Introduction  =head2 Tracing
48    
49  This package provides simple tracing for debugging and reporting purposes. To use it simply call the  This package provides simple tracing for debugging and reporting purposes. To use it simply call the
50  L</TSetup> method to set the options and call L</Trace> to write out trace messages. Each trace  L</TSetup> or L</ETracing> method to set the options and call L</Trace> to write out trace messages.
51  message has a I<trace level> and I<category> associated with it. In addition, the tracing package itself  L</TSetup> and L</ETracing> both establish a I<trace level> and a list of I<categories>. Similarly,
52  has a list of categories and a single trace level set by the B<TSetup> method. Only messages whose trace  each trace message has a I<trace level> and I<category> associated with it. Only messages whose trace
53  level is less than or equal to this package's trace level and whose category is activated will  level is less than or equal to the setup trace level and whose category is activated will
54  be written. Thus, a higher trace level on a message indicates that the message  be written. Thus, a higher trace level on a message indicates that the message
55  is less likely to be seen. A higher trace level passed to B<Setup> means more trace messages will  is less likely to be seen, while a higher trace level passed to B<TSetup> means more trace messages will
56  appear. To generate a trace message, use the following syntax.  appear.
57    
58    =head3 Putting Trace Messages in Your Code
59    
60    To generate a trace message, use the following syntax.
61    
62  C<< Trace($message) if T(errors => 4); >>      Trace($message) if T(errors => 4);
63    
64  This statement will produce a trace message if the trace level is 4 or more and the C<errors>  This statement will produce a trace message if the trace level is 4 or more and the C<errors>
65  category is active. Note that the special category C<main> is always active, so  category is active. There is a special category C<main> that is always active, so
66    
67  C<< Trace($message) if T(main => 4); >>      Trace($message) if T(main => 4);
68    
69  will trace if the trace level is 4 or more.  will trace if the trace level is 4 or more.
70    
# Line 36  Line 72 
72  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is  following call is made in the B<Sprout> package, it will appear if the C<Sprout> category is
73  active and the trace level is 2 or more.  active and the trace level is 2 or more.
74    
75  C<< Trace($message) if T(2); >>      Trace($message) if T(2);
76    
77  To set up tracing, you call the C</Setup> method. The method takes as input a trace level, a list  In scripts, where no package name is available, the category defaults to C<main>.
78  of category names, and a set of options. The trace level and list of category names are  
79    =head3 Custom Tracing
80    
81    Many programs have customized tracing configured using the L</TSetup> method. This is no longer
82    the preferred method, but a knowledge of how custom tracing works can make the more modern
83    L</Emergency Tracing> easier to understand.
84    
85    To set up custom tracing, you call the L</TSetup> method. The method takes as input a trace level,
86    a list of category names, and a destination. The trace level and list of category names are
87  specified as a space-delimited string. Thus  specified as a space-delimited string. Thus
88    
89  C<< TSetup('3 errors Sprout ERDB', 'HTML'); >>      TSetup('3 errors Sprout ERDB', 'TEXT');
90    
91  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and  sets the trace level to 3, activates the C<errors>, C<Sprout>, and C<ERDB> categories, and
92  specifies that messages should be output as HTML paragraphs. The parameters are formatted  specifies that messages should be sent to the standard output.
93  to make it easier to input tracing configuration on a web form.  
94    To turn on tracing for ALL categories, use an asterisk. The call below sets every category to
95    level 3 and writes the output to the standard error output. This sort of thing might be
96    useful in a CGI environment.
97    
98  In addition to HTML and file output for trace messages, you can specify that the trace messages      TSetup('3 *', 'WARN');
99    
100    In addition standard error and file output for trace messages, you can specify that the trace messages
101  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach  be queued. The messages can then be retrieved by calling the L</QTrace> method. This approach
102  is useful if you are building a web page. Instead of having the trace messages interspersed with  is useful if you are building a web page. Instead of having the trace messages interspersed with
103  the page output, they can be gathered together and displayed at the end of the page. This makes  the page output, they can be gathered together and displayed at the end of the page. This makes
104  it easier to debug page formatting problems.  it easier to debug page formatting problems.
105    
106  Finally, you can specify that all trace messages be emitted as warnings.  Finally, you can specify that all trace messages be emitted to a file, or the standard output and
107    a file at the same time. To trace to a file, specify the filename with an output character in front
108    of it.
109    
110        TSetup('4 SQL', ">$fileName");
111    
112    To trace to the standard output and a file at the same time, put a C<+> in front of the angle
113    bracket.
114    
115        TSetup('3 *', "+>$fileName");
116    
117  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.  The flexibility of tracing makes it superior to simple use of directives like C<die> and C<warn>.
118  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.  Tracer calls can be left in the code with minimal overhead and then turned on only when needed.
119  Thus, debugging information is available and easily retrieved even when the application is  Thus, debugging information is available and easily retrieved even when the application is
120  being used out in the field.  being used out in the field.
121    
122    =head3 Trace Levels
123    
124    There is no hard and fast rule on how to use trace levels. The following is therefore only
125    a suggestion.
126    
127    =over 4
128    
129    =item Error 0
130    
131    Message indicates an error that may lead to incorrect results or that has stopped the
132    application entirely.
133    
134    =item Warning 1
135    
136    Message indicates something that is unexpected but that probably did not interfere
137    with program execution.
138    
139    =item Notice 2
140    
141    Message indicates the beginning or end of a major task.
142    
143    =item Information 3
144    
145    Message indicates a subtask. In the FIG system, a subtask generally relates to a single
146    genome. This would be a big loop that is not expected to execute more than 500 times or so.
147    
148    =item Detail 4
149    
150    Message indicates a low-level loop iteration.
151    
152    =back
153    
154    The format of trace messages is important because some utilities analyze trace files.
155    There are three fields-- the time stamp, the category name, and the text.
156    The time stamp is between square brackets and the category name between angle brackets.
157    After the category name there is a colon (C<:>) followed by the message text.
158    If the square brackets or angle brackets are missing, then the trace management
159    utilities assume that they are encountering a set of pre-formatted lines.
160    
161    Note, however, that this formatting is done automatically by the tracing functions. You
162    only need to know about it if you want to parse a trace file.
163    
164    =head3 Emergency Tracing
165    
166    Sometimes, you need a way for tracing to happen automatically without putting parameters
167    in a form or on the command line. Emergency tracing does this. You invoke emergency tracing
168    from the debug form, which is accessed from the [[DebugConsole]]. Emergency tracing requires
169    that you specify a tracing key. For command-line tools, the key is
170    taken from the C<TRACING> environment variable. For web services, the key is taken from
171    a cookie. Either way, the key tells the tracing facility who you are, so that you control
172    the tracing in your environment without stepping on other users.
173    
174    The key can be anything you want. If you don't have a key, the C<SetPassword> page will
175    generate one for you.
176    
177    You can activate and de-activate emergency tracing from the debugging control panel, as
178    well as display the trace file itself.
179    
180    To enable emergency tracing in your code, call
181    
182        ETracing($cgi)
183    
184    from a web script and
185    
186        ETracing()
187    
188    from a command-line script.
189    
190    The web script will look for the tracing key in the cookies, and the command-line
191    script will look for it in the C<TRACING> environment variable. If you are
192    using the L</StandardSetup> method or a [[WebApplication]], emergency tracing
193    will be configured automatically.
194    
195  =cut  =cut
196    
197  # Declare the configuration variables.  # Declare the configuration variables.
198    
199  my $Destination = "NONE";       # Description of where to send the trace output.  my $Destination = "WARN";   # Description of where to send the trace output.
200    my $TeeFlag = 0;            # TRUE if output is going to a file and to the
201                                # standard output
202  my %Categories = ( main => 1 );  my %Categories = ( main => 1 );
203                                                          # hash of active category names                                                          # hash of active category names
204    my @LevelNames = qw(error warn notice info detail);
205  my $TraceLevel = 0;                     # trace level; a higher trace level produces more  my $TraceLevel = 0;                     # trace level; a higher trace level produces more
206                                                          # messages                                                          # messages
207  my @Queue = ();                         # queued list of trace messages.  my @Queue = ();                         # queued list of trace messages.
208  my $LastCategory = "main";  # name of the last category interrogated  my $LastCategory = "main";  # name of the last category interrogated
209    my $LastLevel = 0;          # level of the last test call
210    my $SetupCount = 0;         # number of times TSetup called
211    my $AllTrace = 0;           # TRUE if we are tracing all categories.
212    my $SavedCGI;               # CGI object passed to ETracing
213    my $CommandLine;            # Command line passed to StandardSetup
214    umask 2;                    # Fix the damn umask so everything is group-writable.
215    
216  =head2 Public Methods  =head2 Tracing Methods
217    
218    =head3 Setups
219    
220        my $count = Tracer::Setups();
221    
222    Return the number of times L</TSetup> has been called.
223    
224    This method allows for the creation of conditional tracing setups where, for example, we
225    may want to set up tracing if nobody else has done it before us.
226    
227    =cut
228    
229    sub Setups {
230        return $SetupCount;
231    }
232    
233  =head3 TSetup  =head3 TSetup
234    
235  C<< TSetup($categoryList, $target); >>      TSetup($categoryList, $target);
236    
237  This method is used to specify the trace options. The options are stored as package data  This method is used to specify the trace options. The options are stored as package data
238  and interrogated by the L</Trace> and L</T> methods.  and interrogated by the L</Trace> and L</T> methods.
# Line 93  Line 248 
248    
249  The destination for the trace output. To send the trace output to a file, specify the file  The destination for the trace output. To send the trace output to a file, specify the file
250  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended  name preceded by a ">" symbol. If a double symbol is used (">>"), then the data is appended
251  to the file. Otherwise the file is cleared before tracing begins. In addition to sending  to the file. Otherwise the file is cleared before tracing begins. Precede the first ">"
252  the trace messages to a file, you can specify a special destination. C<HTML> will cause  symbol with a C<+> to echo output to a file AND to the standard output. In addition to
253  tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>  sending the trace messages to a file, you can specify a special destination. C<HTML> will
254    cause tracing to the standard output with each line formatted as an HTML paragraph. C<TEXT>
255  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace  will cause tracing to the standard output as ordinary text. C<ERROR> will cause trace
256  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace  messages to be sent to the standard error output as ordinary text. C<QUEUE> will cause trace
257  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will  messages to be stored in a queue for later retrieval by the L</QTrace> method. C<WARN> will
# Line 113  Line 269 
269          my @categoryData = split /\s+/, $categoryList;          my @categoryData = split /\s+/, $categoryList;
270          # Extract the trace level.          # Extract the trace level.
271          $TraceLevel = shift @categoryData;          $TraceLevel = shift @categoryData;
272          # Build the category hash.      # Presume category-based tracing until we learn otherwise.
273        $AllTrace = 0;
274        # Build the category hash. Note that if we find a "*", we turn on non-category
275        # tracing. We must also clear away any pre-existing data.
276        %Categories = ( main => 1 );
277          for my $category (@categoryData) {          for my $category (@categoryData) {
278                  $Categories{$category} = 1;          if ($category eq '*') {
279                $AllTrace = 1;
280            } else {
281                $Categories{lc $category} = 1;
282            }
283          }          }
284          # Now we need to process the destination information. The most important special          # Now we need to process the destination information. The most important special
285          # case is the single ">", which requires we clear the file first. After doing      # case is when we're writing to a file. This is indicated by ">" (overwrite) and
286          # so, we tack on another ">" sign so that future trace messages are appended.      # ">>" (append). A leading "+" for either indicates that we are also writing to
287        # the standard output (tee mode).
288        if ($target =~ m/^\+?>>?/) {
289            if ($target =~ m/^\+/) {
290                $TeeFlag = 1;
291                $target = substr($target, 1);
292            }
293          if ($target =~ m/^>[^>]/) {          if ($target =~ m/^>[^>]/) {
294                # We need to initialize the file (which clears it).
295                  open TRACEFILE, $target;                  open TRACEFILE, $target;
296                  print TRACEFILE Now() . " Tracing initialized.\n";              print TRACEFILE "[" . Now() . "] [notice] [Tracer] Tracing initialized.\n";
297                  close TRACEFILE;                  close TRACEFILE;
298                # Set to append mode now that the file has been cleared.
299                  $Destination = ">$target";                  $Destination = ">$target";
300          } else {          } else {
301                $Destination = $target;
302            }
303        } else {
304                  $Destination = uc($target);                  $Destination = uc($target);
305          }          }
306        # Increment the setup counter.
307        $SetupCount++;
308  }  }
309    
310  =head3 SetLevel  =head3 SetLevel
311    
312  C<< Tracer::SetLevel($newLevel); >>      Tracer::SetLevel($newLevel);
313    
314  Modify the trace level. A higher trace level will cause more messages to appear.  Modify the trace level. A higher trace level will cause more messages to appear.
315    
# Line 150  Line 327 
327      $TraceLevel = $_[0];      $TraceLevel = $_[0];
328  }  }
329    
330  =head3 Now  =head3 ParseDate
   
 C<< my $string = Tracer::Now(); >>  
   
 Return a displayable time stamp containing the local time.  
   
 =cut  
   
 sub Now {  
         my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);  
         my $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .  
                                  _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);  
         return $retVal;  
 }  
   
 # Pad a number to 2 digits.  
 sub _p2 {  
         my ($value) = @_;  
         $value = "0$value" if ($value < 10);  
         return $value;  
 }  
   
 =head3 LogErrors  
   
 C<< Tracer::LogErrors($fileName); >>  
   
 Route the standard error output to a log file.  
   
 =over 4  
   
 =item fileName  
   
 Name of the file to receive the error output.  
   
 =back  
331    
332  =cut      my $time = Tracer::ParseDate($dateString);
333    
334  sub LogErrors {  Convert a date into a PERL time number. This method expects a date-like string
335          # Get the file name.  and parses it into a number. The string must be vaguely date-like or it will
336          my ($fileName) = @_;  return an undefined value. Our requirement is that a month and day be
337          # Open the file as the standard error output.  present and that three pieces of the date string (time of day, month and day,
338          open STDERR, '>', $fileName;  year) be separated by likely delimiters, such as spaces, commas, and such-like.
 }  
339    
340  =head3 ReadOptions  If a time of day is present, it must be in military time with two digits for
341    everything but the hour.
342    
343  C<< my %options = Tracer::ReadOptions($fileName); >>  The year must be exactly four digits.
344    
345  Read a set of options from a file. Each option is encoded in a line of text that has the  Additional stuff can be in the string. We presume it's time zones or weekdays or something
346  format  equally innocuous. This means, however, that a sufficiently long sentence with date-like
347    parts in it may be interpreted as a date. Hopefully this will not be a problem.
348    
349  I<optionName>C<=>I<optionValue>C<; >I<comment>  It should be guaranteed that this method will parse the output of the L</Now> function.
350    
351  The option name must consist entirely of letters, digits, and the punctuation characters  The parameters are as follows.
 C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank  
 character is a semi-colon will be ignored. The return hash will map each option name to  
 the corresponding option value.  
352    
353  =over 4  =over 4
354    
355  =item fileName  =item dateString
356    
357  Name of the file containing the option data.  The date string to convert.
358    
359  =item RETURN  =item RETURN
360    
361  Returns a hash mapping the option names specified in the file to their corresponding option  Returns a PERL time, that is, a number of seconds since the epoch, or C<undef> if
362  value.  the date string is invalid. A valid date string must contain a month and day.
363    
364  =back  =back
365    
366  =cut  =cut
367    
368  sub ReadOptions {  # Universal month conversion table.
369          # Get the parameters.  use constant MONTHS => {    Jan =>  0, January   =>  0, '01' =>  0,  '1' =>  0,
370          my ($fileName) = @_;                              Feb =>  1, February  =>  1, '02' =>  1,  '2' =>  1,
371          # Open the file.                              Mar =>  2, March     =>  2, '03' =>  2,  '3' =>  2,
372          (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");                              Apr =>  3, April     =>  3, '04' =>  3,  '4' =>  3,
373          # Count the number of records read.                              May =>  4, May       =>  4, '05' =>  4,  '5' =>  4,
374          my ($records, $comments) = 0;                              Jun =>  5, June      =>  5, '06' =>  5,  '6' =>  5,
375          # Create the return hash.                              Jul =>  6, July      =>  6, '07' =>  6,  '7' =>  6,
376          my %retVal = ();                              Aug =>  7, August    =>  7, '08' =>  7,  '8' =>  7,
377          # Loop through the file, accumulating key-value pairs.                              Sep =>  8, September =>  8, '09' =>  8,  '9' =>  8,
378          while (my $line = <CONFIGFILE>) {                              Oct =>  9, October  =>   9, '10' =>  9,
379                  # Denote we've read a line.                              Nov => 10, November =>  10, '11' => 10,
380                  $records++;                              Dec => 11, December =>  11, '12' => 11
381                  # Determine the line type.                          };
                 if ($line =~ /^\s*[\n\r]/) {  
                         # A blank line is a comment.  
                         $comments++;  
                 } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {  
                         # Here we have an option assignment.  
                         retVal{$1} = $2;  
                 } elsif ($line =~ /^\s*;/) {  
                         # Here we have a text comment.  
                         $comments++;  
                 } else {  
                         # Here we have an invalid line.  
                         Trace("Invalid option statement in record $records.") if T(0);  
                 }  
         }  
         # Return the hash created.  
         return %retVal;  
 }  
   
 =head3 GetOptions  
   
 C<< Tracer::GetOptions(\%defaults, \%options); >>  
   
 Merge a specified set of options into a table of defaults. This method takes two hash references  
 as input and uses the data from the second to update the first. If the second does not exist,  
 there will be no effect. An error will be thrown if one of the entries in the second hash does not  
 exist in the first.  
   
 Consider the following example.  
   
 C<< my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options); >>  
   
 In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and  
 B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of  
 B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and  
 the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level  
 will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as  
   
 C<< {databaseType => 'Oracle'} >>  
   
 an error will occur because the B<databaseType> option does not exist.  
   
 =over 4  
   
 =item defaults  
   
 Table of default option values.  
   
 =item options  
   
 Table of overrides, if any.  
   
 =item RETURN  
   
 Returns a reference to the default table passed in as the first parameter.  
   
 =back  
   
 =cut  
382    
383  sub GetOptions {  sub ParseDate {
384          # Get the parameters.          # Get the parameters.
385          my ($defaults, $options) = @_;      my ($dateString) = @_;
386          # Check for overrides.      # Declare the return variable.
387          if ($options) {      my $retVal;
388                  # Loop through the overrides.      # Find the month and day of month. There are two ways that can happen. We check for the
389                  while (my ($option, $setting) = each %{$options}) {      # numeric style first. That way, if the user's done something like "Sun 12/22", then we
390                          # Insure this override exists.      # won't be fooled into thinking the month is Sunday.
391                          if (!exists $defaults->{$option}) {      if ($dateString =~ m#\b(\d{1,2})/(\d{1,2})\b# || $dateString =~ m#\b(\w+)\s(\d{1,2})\b#) {
392                                  croak "Unrecognized option $option encountered.";          my ($mon, $mday) = (MONTHS->{$1}, $2);
393            # Insist that the month and day are valid.
394            if (defined($mon) && $2 >= 1 && $2 <= 31) {
395                # Find the time.
396                my ($hour, $min, $sec) = (0, 0, 0);
397                if ($dateString =~ /\b(\d{1,2}):(\d{2}):(\d{2})\b/) {
398                    ($hour, $min, $sec) = ($1, $2, $3);
399                }
400                # Find the year.
401                my $year;
402                if ($dateString =~ /\b(\d{4})\b/) {
403                    $year = $1;
404                          } else {                          } else {
405                                  # Apply the override.                  # Get the default year, which is this one. Note we must convert it to
406                                  $defaults->{$option} = $setting;                  # the four-digit value expected by "timelocal".
407                    (undef, undef, undef, undef, undef, $year) = localtime();
408                    $year += 1900;
409                          }                          }
410                $retVal = timelocal($sec, $min, $hour, $mday, $mon, $year);
411                  }                  }
412          }          }
413          # Return the merged table.      # Return the result.
414          return $defaults;      return $retVal;
415  }  }
416    
417  =head3 MergeOptions  =head3 LogErrors
418    
419  C<< Tracer::MergeOptions(\%table, \%defaults); >>      Tracer::LogErrors($fileName);
420    
421  Merge default values into a hash table. This method looks at the key-value pairs in the  Route the standard error output to a log file.
 second (default) hash, and if a matching key is not found in the first hash, the default  
 pair is copied in. The process is similar to L</GetOptions>, but there is no error-  
 checking and no return value.  
422    
423  =over 4  =over 4
424    
425  =item table  =item fileName
   
 Hash table to be updated with the default values.  
   
 =item defaults  
426    
427  Default values to be merged into the first hash table if they are not already present.  Name of the file to receive the error output.
428    
429  =back  =back
430    
431  =cut  =cut
432    
433  sub MergeOptions {  sub LogErrors {
434          # Get the parameters.      # Get the file name.
435          my ($table, $defaults) = @_;      my ($fileName) = @_;
436          # Loop through the defaults.      # Open the file as the standard error output.
437          while (my ($key, $value) = each %{$defaults}) {      open STDERR, '>', $fileName;
                 if (!exists $table->{$key}) {  
                         $table->{$key} = $value;  
                 }  
         }  
438  }  }
439    
440  =head3 Trace  =head3 Trace
441    
442  C<< Trace($message); >>      Trace($message);
443    
444  Write a trace message to the target location specified in L</TSetup>. If there has not been  Write a trace message to the target location specified in L</TSetup>. If there has not been
445  any prior call to B<TSetup>.  any prior call to B<TSetup>.
# Line 371  Line 457 
457  sub Trace {  sub Trace {
458          # Get the parameters.          # Get the parameters.
459          my ($message) = @_;          my ($message) = @_;
460        # Strip off any line terminators at the end of the message. We will add
461        # new-line stuff ourselves.
462        my $stripped = Strip($message);
463        # Compute the caller information.
464        my ($callPackage, $callFile, $callLine) = caller();
465        my $callFileTitle = basename($callFile);
466        # Check the caller.
467        my $callerInfo = ($callFileTitle ne "Tracer.pm" ? " [$callFileTitle $callLine]" : "");
468          # Get the timestamp.          # Get the timestamp.
469          my $timeStamp = Now();          my $timeStamp = Now();
470          # Format the message. Note we strip off any line terminators at the end.      # Build the prefix.
471          my $formatted = "$timeStamp <$LastCategory>: " . Strip($message);      my $level = $LevelNames[$LastLevel] || "($LastLevel)";
472        my $prefix = "[$timeStamp] [$level] [$LastCategory]$callerInfo";
473        # Format the message.
474        my $formatted = "$prefix $stripped";
475          # Process according to the destination.          # Process according to the destination.
476          if ($Destination eq "TEXT") {          if ($Destination eq "TEXT") {
477                  # Write the message to the standard output.                  # Write the message to the standard output.
478                  print "$formatted\n";                  print "$formatted\n";
479          } elsif ($Destination eq "ERROR") {          } elsif ($Destination eq "ERROR") {
480                  # Write the message to the error output.          # Write the message to the error output. Here, we want our prefix fields.
481                  print STDERR "$formatted\n";                  print STDERR "$formatted\n";
482        } elsif ($Destination eq "WARN") {
483            # Emit the message to the standard error output. It is presumed that the
484            # error logger will add its own prefix fields, the notable exception being
485            # the caller info.
486            print STDERR "$callerInfo$stripped\n";
487          } elsif ($Destination eq "QUEUE") {          } elsif ($Destination eq "QUEUE") {
488                  # Push the message into the queue.                  # Push the message into the queue.
489                  push @Queue, "$formatted";                  push @Queue, "$formatted";
490          } elsif ($Destination eq "HTML") {          } elsif ($Destination eq "HTML") {
491                  # Convert the message to HTML and write it to the standard output.                  # Convert the message to HTML and write it to the standard output.
492                  my $escapedMessage = CGI::escapeHTML($message);          my $escapedMessage = CGI::escapeHTML($stripped);
493                  print "<p>$formatted</p>\n";          print "<p>$timeStamp $LastCategory $LastLevel: $escapedMessage</p>\n";
     } elsif ($Destination eq "WARN") {  
        # Emit the message as a warning.  
        warn $message;  
494          } elsif ($Destination =~ m/^>>/) {          } elsif ($Destination =~ m/^>>/) {
495                  # Write the trace message to an output file.                  # Write the trace message to an output file.
496                  open TRACING, $Destination;          open(TRACING, $Destination) || die "Tracing open for \"$Destination\" failed: $!";
497            # Lock the file.
498            flock TRACING, LOCK_EX;
499                  print TRACING "$formatted\n";                  print TRACING "$formatted\n";
500                  close TRACING;                  close TRACING;
501            # If the Tee flag is on, echo it to the standard output.
502            if ($TeeFlag) {
503                print "$formatted\n";
504          }          }
505  }  }
506    }
507    
508    =head3 TraceDump
509    
510        TraceDump($title, $object);
511    
512    Dump an object to the trace log. This method simply calls the C<Dumper>
513    function, but routes the output to the trace log instead of returning it
514    as a string. The output is arranged so that it comes out monospaced when
515    it appears in an HTML trace dump.
516    
517    =over 4
518    
519    =item title
520    
521    Title to give to the object being dumped.
522    
523    =item object
524    
525    Reference to a list, hash, or object to dump.
526    
527    =back
528    
529    =cut
530    
531    sub TraceDump {
532        # Get the parameters.
533        my ($title, $object) = @_;
534        # Trace the object.
535        Trace("Object dump for $title:\n" . Dumper($object));
536    }
537    
538  =head3 T  =head3 T
539    
540  C<< my $switch = T($category, $traceLevel); >>      my $switch = T($category, $traceLevel);
541    
542          or          or
543    
544  C<< my $switch = T($traceLevel); >>      my $switch = T($traceLevel);
545    
546  Return TRUE if the trace level is at or above a specified value and the specified category  Return TRUE if the trace level is at or above a specified value and the specified category
547  is active, else FALSE. If no category is specified, the caller's package name is used.  is active, else FALSE. If no category is specified, the caller's package name is used.
# Line 439  Line 574 
574                  my ($category, $traceLevel) = @_;                  my ($category, $traceLevel) = @_;
575                  if (!defined $traceLevel) {                  if (!defined $traceLevel) {
576                          # Here we have no category, so we need to get the calling package.                          # Here we have no category, so we need to get the calling package.
577                # The calling package is normally the first parameter. If it is
578                # omitted, the first parameter will be the tracelevel. So, the
579                # first thing we do is shift the so-called category into the
580                # $traceLevel variable where it belongs.
581                          $traceLevel = $category;                          $traceLevel = $category;
582                          my ($package, $fileName, $line) = caller;                          my ($package, $fileName, $line) = caller;
583              # If there is no calling package, we default to "main".              # If there is no calling package, we default to "main".
584                          if (!$package) {                          if (!$package) {
585                  $category = "main";                  $category = "main";
586                          } else {                          } else {
587                                  $category = $package;                  my @cats = split /::/, $package;
588                    $category = $cats[$#cats];
589                          }                          }
590                  }                  }
591          # Save the category name.          # Save the category name and level.
592          $LastCategory = $category;          $LastCategory = $category;
593                  # Use the category and tracelevel to compute the result.          $LastLevel = $traceLevel;
594                  $retVal = ($traceLevel <= $TraceLevel && exists $Categories{$category});          # Convert it to lower case before we hash it.
595            $category = lc $category;
596            # Validate the trace level.
597            if (ref $traceLevel) {
598                Confess("Bad trace level.");
599            } elsif (ref $TraceLevel) {
600                Confess("Bad trace config.");
601            }
602            # Make the check. Note that level 0 shows even if the category is turned off.
603            $retVal = ($traceLevel <= $TraceLevel && ($traceLevel == 0 || $AllTrace || exists $Categories{$category}));
604      }      }
605          # Return the computed result.          # Return the computed result.
606      return $retVal;      return $retVal;
607  }  }
608    
609  =head3 ParseCommand  =head3 QTrace
   
 C<< my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList); >>  
   
 Parse a command line consisting of a list of parameters. The initial parameters may be option  
 specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped  
 off and merged into a table of default options. The remainder of the command line is  
 returned as a list of positional arguments. For example, consider the following invocation.  
610    
611  C<< my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words); >>      my $data = QTrace($format);
612    
613  In this case, the list @words will be treated as a command line. There are two options available,  Return the queued trace data in the specified format.
 B<errors> and B<logFile>. If @words has the following format  
614    
615  C<< -logFile=error.log apple orange rutabaga >>  =over 4
616    
617  then at the end of the invocation, C<$options> will be  =item format
618    
619  C<< { errors => 0, logFile => 'error.log' } >>  C<html> to format the data as an HTML list, C<text> to format it as straight text.
620    
621  and C<@arguments> will contain  =back
622    
623  C<< apple orange rutabaga >>  =cut
624    
625  The parser allows for some escape sequences. See L</UnEscape> for a description. There is no  sub QTrace {
626  support for quote characters.      # Get the parameter.
627        my ($format) = @_;
628        # Create the return variable.
629        my $retVal = "";
630        # Only proceed if there is an actual queue.
631        if (@Queue) {
632            # Process according to the format.
633            if ($format =~ m/^HTML$/i) {
634                # Convert the queue into an HTML list.
635                $retVal = "<ul>\n";
636                for my $line (@Queue) {
637                    my $escapedLine = CGI::escapeHTML($line);
638                    $retVal .= "<li>$escapedLine</li>\n";
639                }
640                $retVal .= "</ul>\n";
641            } elsif ($format =~ m/^TEXT$/i) {
642                # Convert the queue into a list of text lines.
643                $retVal = join("\n", @Queue) . "\n";
644            }
645            # Clear the queue.
646            @Queue = ();
647        }
648        # Return the formatted list.
649        return $retVal;
650    }
651    
652    =head3 Confess
653    
654        Confess($message);
655    
656    Trace the call stack and abort the program with the specified message. When used with
657    the OR operator and the L</Assert> method, B<Confess> can function as a debugging assert.
658    So, for example
659    
660        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
661    
662    Will abort the program with a stack trace if the value of C<$recNum> is negative.
663    
664    =over 4
665    
666    =item message
667    
668    Message to include in the trace.
669    
670    =back
671    
672    =cut
673    
674    sub Confess {
675        # Get the parameters.
676        my ($message) = @_;
677        # Set up the category and level.
678        $LastCategory = "(confess)";
679        $LastLevel = 0;
680        # Trace the call stack.
681        Cluck($message);
682        # Abort the program.
683        croak(">>> $message");
684    }
685    
686    =head3 SaveCGI
687    
688        Tracer::SaveCGI($cgi);
689    
690    This method saves the CGI object but does not activate emergency tracing.
691    It is used to allow L</Warn> to work in situations where emergency
692    tracing is contra-indicated (e.g. the wiki).
693    
694    =over 4
695    
696    =item cgi
697    
698    Active CGI query object.
699    
700    =back
701    
702    =cut
703    
704    sub SaveCGI {
705        $SavedCGI = $_[0];
706    }
707    
708    =head3 Warn
709    
710        Warn($message, @options);
711    
712    This method traces an important message. If an RSS feed is configured
713    (via I<FIG_Config::error_feed>) and the tracing destination is C<WARN>,
714    then the message will be echoed to the feed. In general, a tracing
715    destination of C<WARN> indicates that the caller is running as a web
716    service in a production environment; however, this is not a requirement.
717    
718    To force warnings into the RSS feed even when the tracing destination
719    is not C<WARN>, simply specify the C<Feed> tracing module. This can be
720    configured automatically when L</StandardSetup> is used.
721    
722    The L</Cluck> method calls this one for its final message. Since
723    L</Confess> calls L</Cluck>, this means that any error which is caught
724    and confessed will put something in the feed. This insures that someone
725    will be alerted relatively quickly when a failure occurs.
726    
727    =over 4
728    
729    =item message
730    
731    Message to be traced.
732    
733    =item options
734    
735    A list containing zero or more options.
736    
737    =back
738    
739    The permissible options are as follows.
740    
741    =over 4
742    
743    =item noStack
744    
745    If specified, then the stack trace is not included in the output.
746    
747    =back
748    
749    =cut
750    
751    sub Warn {
752        # Get the parameters.
753        my $message = shift @_;
754        my %options = map { $_ => 1 } @_;
755        # Save $@;
756        my $savedError = $@;
757        # Trace the message.
758        Trace($message);
759        # This will contain the lock handle. If it's defined, it means we need to unlock.
760        my $lock;
761        # Check for feed forcing.
762        my $forceFeed = exists $Categories{feed};
763        # An error here would be disastrous. Note that if debug mode is specified,
764        # we do this stuff even in a test environment.
765        eval {
766            # Do we need to put this in the RSS feed?
767            if ($FIG_Config::error_feed && ($Destination eq 'WARN' || $forceFeed)) {
768                # Probably. We need to check first, however, to see if it's from an
769                # ignored IP. For non-CGI situations, we default the IP to the self-referent.
770                my $key = "127.0.0.1";
771                if (defined $SavedCGI) {
772                    # Get the IP address.
773                    $key = $ENV{HTTP_X_FORWARDED_FOR} || $ENV{REMOTE_ADDR};
774                }
775                # Is the IP address in the ignore list?
776                my $found = scalar(grep { $_ eq $key } @FIG_Config::error_ignore_ips);
777                if (! $found) {
778                    # No. We're good. We now need to compute the date, the link, and the title.
779                    # First, the date, in a very specific format.
780                    my $date = strftime("%a, %02e %b %H:%M:%S %Y ", localtime) .
781                        (tz_local_offset() / 30);
782                    # Environment data goes in here. We start with the date.
783                    my $environment = "$date.  ";
784                    # If we need to recap the message (because it's too long to be a title), we'll
785                    # put it in here.
786                    my $recap;
787                    # Copy the message and remove excess space.
788                    my $title = $message;
789                    $title =~ s/\s+/ /gs;
790                    # If it's too long, we have to split it up.
791                    if (length $title > 60) {
792                        # Put the full message in the environment string.
793                        $recap = $title;
794                        # Excerpt it as the title.
795                        $title = substr($title, 0, 50) . "...";
796                    }
797                    # If we have a CGI object, then this is a web error. Otherwise, it's
798                    # command-line.
799                    if (defined $SavedCGI) {
800                        # We're in a web service. The environment is the user's IP, and the link
801                        # is the URL that got us here.
802                        $environment .= "Event Reported at IP address $key process $$.";
803                        my $url = $SavedCGI->self_url();
804                        # We need the user agent string and (if available) the referrer.
805                        # The referrer will be the link.
806                        $environment .= " User Agent $ENV{HTTP_USER_AGENT}";
807                        if ($ENV{HTTP_REFERER}) {
808                            my $link = $ENV{HTTP_REFERER};
809                            $environment .= " referred from <a href=\"$link\">$link</a>.";
810                        } else {
811                            $environment .= " referrer unknown.";
812                        }
813                        # Close off the sentence with the original link.
814                        $environment .= " URL of event is <a href=\"$url\">$url</a>.";
815                    } else {
816                        # No CGI object, so we're a command-line tool. Use the tracing
817                        # key and the PID as the user identifier, and add the command.
818                        my $key = EmergencyKey();
819                        $environment .= "Event Reported by $key process $$.";
820                        if ($CommandLine) {
821                            # We're in a StandardSetup script, so we have the real command line.
822                            $environment .= "\n<pre>" . CGI::escapeHTML($CommandLine) . "</pre>\n";
823                        } elsif ($ENV{_}) {
824                            # We're in a BASH script, so the command has been stored in the _ variable.
825                            $environment .= "  Command = " . CGI::escapeHTML($ENV{_}) . "\n";
826                        }
827                    }
828                    # Build a GUID. We use the current time, the title, and the process ID,
829                    # then digest the result.
830                    my $guid = Digest::MD5::md5_base64(gettimeofday(), $title, $$);
831                    # Finally, the description. This is a stack trace plus various environmental stuff.
832                    # The trace is optional.
833                    my $stackTrace;
834                    if ($options{noStack}) {
835                        $stackTrace = "";
836                    } else {
837                        my @trace = LongMess();
838                        # Only proceed if we got something back.
839                        if (scalar(@trace) > 0) {
840                            $trace[0] =~ s/Tracer::Warn.+?called/Event occurred/;
841                            $stackTrace = "Stack trace:<pre>" . join("\n", @trace, "</pre>");
842                        }
843                    }
844                    # We got the stack trace. Now it's time to put it all together.
845                    # We have a goofy thing here in that we need to HTML-escape some sections of the description
846                    # twice. They will be escaped once here, and then once when written by XML::Simple. They are
847                    # unescaped once when processed by the RSS reader, and stuff in the description is treated as
848                    # HTML. So, anything escaped here is treated as a literal when viewed in the RSS reader, but
849                    # our <br>s and <pre>s are used to format the description.
850                    $recap = (defined $recap ? "<em>" . CGI::escapeHTML($recap) . "</em><br /><br />" : "");
851                    my $description = "$recap$environment  $stackTrace";
852                    # Okay, we have all the pieces. Create a hash of the new event.
853                    my $newItem = { title => $title,
854                                    description => $description,
855                                    category => $LastCategory,
856                                    pubDate => $date,
857                                    guid => $guid,
858                                  };
859                    # We need XML capability for this.
860                    require XML::Simple;
861                    # The RSS document goes in here.
862                    my $rss;
863                    # Get the name of the RSS file. It's in the FIG temporary directory.
864                    my $fileName = "$FIG_Config::temp/$FIG_Config::error_feed";
865                    # Open the config file and lock it.
866                    $lock = Open(undef, "<$FIG_Config::fig_disk/config/FIG_Config.pm");
867                    flock $lock, LOCK_EX;
868                    # Does it exist?
869                    if (-s $fileName) {
870                        # Slurp it in.
871                        $rss = XML::Simple::XMLin($fileName, ForceArray => ['item']);
872                    } else {
873                        my $size = -s $fileName;
874                        # Create an empty channel.
875                        $rss = {
876                            channel => {
877                                title => 'NMPDR Warning Feed',
878                                link => "$FIG_Config::temp_url/$FIG_Config::error_feed",
879                                description => "Important messages regarding the status of the NMPDR.",
880                                generator => "NMPDR Trace Facility",
881                                docs => "http://blogs.law.harvard.edu/tech/rss",
882                                item => []
883                            },
884                        };
885                    }
886                    # Get the channel object.
887                    my $channel = $rss->{channel};
888                    # Update the last-build date.
889                    $channel->{lastBuildDate} = $date;
890                    # Get the item array.
891                    my $items = $channel->{item};
892                    # Insure it has only 100 entries.
893                    while (scalar @{$items} > 100) {
894                        pop @{$items};
895                    }
896                    # Add our new item at the front.
897                    unshift @{$items}, $newItem;
898                    # Create the XML. Note we do not include the root or the declaration. XML Simple can't handle
899                    # the requirements for those.
900                    my $xml = XML::Simple::XMLout($channel, NoAttr => 1, RootName => 'channel', XmlDecl => '');
901                    # Here we put in the root and declaration. The problem is that the root has to have the version attribute
902                    # in it. So, we suppress the root and do it by hand, and that requires suppressing the declaration, too.
903                    $xml = "<?xml version=\"1.0\" encoding=\"utf-8\"?>\n<rss version=\"2.0\">$xml\n</rss>";
904                    # We don't use Open here because we can't afford an error.
905                    if (open XMLOUT, ">$fileName") {
906                        print XMLOUT $xml;
907                        close XMLOUT;
908                    }
909                }
910            }
911        };
912        if ($@) {
913            # If the feed failed, we need to know why. The error will be traced, but this method will not be involved
914            # (which is a good thing).
915            my $error = $@;
916            Trace("Feed Error: $error") if T(Feed => 0);
917        }
918        # Be sure to unlock.
919        if ($lock) {
920            flock $lock, LOCK_UN;
921            undef $lock;
922        }
923        # Restore the error message.
924        $@ = $savedError;
925    }
926    
927    
928    
929    
930    =head3 Assert
931    
932        Assert($condition1, $condition2, ... $conditionN);
933    
934    Return TRUE if all the conditions are true. This method can be used in conjunction with
935    the OR operator and the L</Confess> method as a debugging assert.
936    So, for example
937    
938        Assert($recNum >= 0) || Confess("Invalid record number $recNum.");
939    
940    Will abort the program with a stack trace if the value of C<$recNum> is negative.
941    
942    =cut
943    sub Assert {
944        my $retVal = 1;
945        LOOP: for my $condition (@_) {
946            if (! $condition) {
947                $retVal = 0;
948                last LOOP;
949            }
950        }
951        return $retVal;
952    }
953    
954    =head3 Cluck
955    
956        Cluck($message);
957    
958    Trace the call stack. Note that for best results, you should qualify the call with a
959    trace condition. For example,
960    
961        Cluck("Starting record parse.") if T(3);
962    
963    will only trace the stack if the trace level for the package is 3 or more.
964    
965    =over 4
966    
967    =item message
968    
969    Message to include in the trace.
970    
971    =back
972    
973    =cut
974    
975    sub Cluck {
976        # Get the parameters.
977        my ($message) = @_;
978        # Trace what's happening.
979        Trace("Stack trace for event: $message");
980        # Get the stack trace.
981        my @trace = LongMess();
982        # Convert the trace to a series of messages.
983        for my $line (@trace) {
984            # Replace the tab at the beginning with spaces.
985            $line =~ s/^\t/    /;
986            # Trace the line.
987            Trace($line);
988        }
989        # Issue a warning. This displays the event message and inserts it into the RSS error feed.
990        Warn($message);
991    }
992    
993    =head3 LongMess
994    
995        my @lines = Tracer::LongMess();
996    
997    Return a stack trace with all tracing methods removed. The return will be in the form of a list
998    of message strings.
999    
1000    =cut
1001    
1002    sub LongMess {
1003        # Declare the return variable.
1004        my @retVal = ();
1005        my $confession = longmess("");
1006        for my $line (split /\s*\n/, $confession) {
1007            unless ($line =~ /Tracer\.pm/) {
1008                # Here we have a line worth keeping. Push it onto the result list.
1009                push @retVal, $line;
1010            }
1011        }
1012        # Return the result.
1013        return @retVal;
1014    }
1015    
1016    =head3 ETracing
1017    
1018        ETracing($parameter);
1019    
1020    Set up emergency tracing. Emergency tracing is tracing that is turned
1021    on automatically for any program that calls this method. The emergency
1022    tracing parameters are stored in a a file identified by a tracing key.
1023    If this method is called with a CGI object, then the tracing key is
1024    taken from a cookie. If it is called with no parameters, then the tracing
1025    key is taken from an environment variable. If it is called with a string,
1026    the tracing key is that string.
1027    
1028    =over 4
1029    
1030    =item parameter
1031    
1032    A parameter from which the tracing key is computed. If it is a scalar,
1033    that scalar is used as the tracing key. If it is a CGI object, the
1034    tracing key is taken from the C<IP> cookie. If it is omitted, the
1035    tracing key is taken from the C<TRACING> environment variable. If it
1036    is a CGI object and emergency tracing is not on, the C<Trace> and
1037    C<TF> parameters will be used to determine the type of tracing.
1038    
1039    =back
1040    
1041    =cut
1042    
1043    sub ETracing {
1044        # Get the parameter.
1045        my ($parameter) = @_;
1046        # Check for CGI mode.
1047        if (defined $parameter && ref $parameter eq 'CGI') {
1048            $SavedCGI = $parameter;
1049        } else {
1050            $SavedCGI = undef;
1051        }
1052        # Default to no tracing except errors.
1053        my ($tracing, $dest) = ("0", "WARN");
1054        # Check for emergency tracing.
1055        my $tkey = EmergencyKey($parameter);
1056        my $emergencyFile = EmergencyFileName($tkey);
1057        if (-e $emergencyFile) {
1058            # We have the file. Read in the data.
1059            my @tracing = GetFile($emergencyFile);
1060            # Pull off the time limit.
1061            my $expire = shift @tracing;
1062            # Convert it to seconds.
1063            $expire *= 3600;
1064            # Check the file data.
1065            my $stat = stat($emergencyFile);
1066            my ($now) = gettimeofday;
1067            if ($now - $stat->mtime > $expire) {
1068                # Delete the expired file.
1069                unlink $emergencyFile;
1070            } else {
1071                # Emergency tracing is on. Pull off the destination and
1072                # the trace level;
1073                $dest = shift @tracing;
1074                my $level = shift @tracing;
1075                # Convert the destination to a real tracing destination.
1076                # temp directory.
1077                $dest = EmergencyTracingDest($tkey, $dest);
1078                # Insure Tracer is specified.
1079                my %moduleHash = map { $_ => 1 } @tracing;
1080                $moduleHash{Tracer} = 1;
1081                # Set the trace parameter.
1082                $tracing = join(" ", $level, sort keys %moduleHash);
1083            }
1084        } elsif (defined $SavedCGI) {
1085            # There's no emergency tracing, but we have a CGI object, so check
1086            # for tracing from the form parameters.
1087            if ($SavedCGI->param('Trace')) {
1088                # Here the user has requested tracing via a form.
1089                $dest = ($SavedCGI->param('TF') ? ">$FIG_Config::temp/Trace$$.log" : "QUEUE");
1090                $tracing = $SavedCGI->param('Trace') . " Tracer";
1091            }
1092        }
1093        # Setup the tracing we've determined from all the stuff above.
1094        TSetup($tracing, $dest);
1095        # Check to see if we're a web script.
1096        if (defined $SavedCGI) {
1097            # Yes we are. Trace the form and environment data.
1098            TraceParms($SavedCGI);
1099            # Check for RAW mode. In raw mode, we print a fake header so that we see everything
1100            # emitted by the script in its raw form.
1101            if (T(Raw => 3)) {
1102                print CGI::header(-type => 'text/plain', -tracing => 'Raw');
1103            }
1104        }
1105    }
1106    
1107    =head3 EmergencyFileName
1108    
1109        my $fileName = Tracer::EmergencyFileName($tkey);
1110    
1111    Return the emergency tracing file name. This is the file that specifies
1112    the tracing information.
1113    
1114    =over 4
1115    
1116    =item tkey
1117    
1118    Tracing key for the current program.
1119    
1120    =item RETURN
1121    
1122    Returns the name of the file to contain the emergency tracing information.
1123    
1124    =back
1125    
1126    =cut
1127    
1128    sub EmergencyFileName {
1129        # Get the parameters.
1130        my ($tkey) = @_;
1131        # Compute the emergency tracing file name.
1132        return "$FIG_Config::temp/Emergency$tkey.txt";
1133    }
1134    
1135    =head3 EmergencyFileTarget
1136    
1137        my $fileName = Tracer::EmergencyFileTarget($tkey);
1138    
1139    Return the emergency tracing target file name. This is the file that receives
1140    the tracing output for file-based tracing.
1141    
1142    =over 4
1143    
1144    =item tkey
1145    
1146    Tracing key for the current program.
1147    
1148    =item RETURN
1149    
1150    Returns the name of the file to contain the trace output.
1151    
1152    =back
1153    
1154    =cut
1155    
1156    sub EmergencyFileTarget {
1157        # Get the parameters.
1158        my ($tkey) = @_;
1159        # Compute the emergency tracing file name.
1160        return "$FIG_Config::temp/trace$tkey.log";
1161    }
1162    
1163    =head3 EmergencyTracingDest
1164    
1165        my $dest = Tracer::EmergencyTracingDest($tkey, $myDest);
1166    
1167    This method converts an emergency tracing destination to a real
1168    tracing destination. The main difference is that if the
1169    destination is C<FILE> or C<APPEND>, we convert it to file
1170    output. If the destination is C<DUAL>, we convert it to file
1171    and standard output.
1172    
1173    =over 4
1174    
1175    =item tkey
1176    
1177    Tracing key for this environment.
1178    
1179    =item myDest
1180    
1181    Destination from the emergency tracing file.
1182    
1183    =item RETURN
1184    
1185    Returns a destination that can be passed into L</TSetup>.
1186    
1187    =back
1188    
1189    =cut
1190    
1191    sub EmergencyTracingDest {
1192        # Get the parameters.
1193        my ($tkey, $myDest) = @_;
1194        # Declare the return variable.
1195        my $retVal = $myDest;
1196        # Process according to the destination value.
1197        if ($myDest eq 'FILE') {
1198            $retVal = ">" . EmergencyFileTarget($tkey);
1199        } elsif ($myDest eq 'APPEND') {
1200            $retVal = ">>" . EmergencyFileTarget($tkey);
1201        } elsif ($myDest eq 'DUAL') {
1202            $retVal = "+>" . EmergencyFileTarget($tkey);
1203        } elsif ($myDest eq 'WARN') {
1204            $retVal = "WARN";
1205        }
1206        # Return the result.
1207        return $retVal;
1208    }
1209    
1210    =head3 Emergency
1211    
1212        Emergency($key, $hours, $dest, $level, @modules);
1213    
1214    Turn on emergency tracing. This method is normally invoked over the web from
1215    a debugging console, but it can also be called by the C<trace.pl> script.
1216    The caller specifies the duration of the emergency in hours, the desired tracing
1217    destination, the trace level, and a list of the trace modules to activate.
1218    For the length of the duration, when a program in an environment with the
1219    specified tracing key active invokes a Sprout CGI script, tracing will be
1220    turned on automatically. See L</TSetup> for more about tracing setup and
1221    L</ETracing> for more about emergency tracing.
1222    
1223    =over 4
1224    
1225    =item tkey
1226    
1227    The tracing key. This is used to identify the control file and the trace file.
1228    
1229    =item hours
1230    
1231    Number of hours to keep emergency tracing alive.
1232    
1233    =item dest
1234    
1235    Tracing destination. If no path information is specified for a file
1236    destination, it is put in the FIG temporary directory.
1237    
1238    =item level
1239    
1240    Tracing level. A higher level means more trace messages.
1241    
1242    =item modules
1243    
1244    A list of the tracing modules to activate.
1245    
1246    =back
1247    
1248    =cut
1249    
1250    sub Emergency {
1251        # Get the parameters.
1252        my ($tkey, $hours, $dest, $level, @modules) = @_;
1253        # Create the emergency file.
1254        my $specFile = EmergencyFileName($tkey);
1255        my $outHandle = Open(undef, ">$specFile");
1256        print $outHandle join("\n", $hours, $dest, $level, @modules, "");
1257    }
1258    
1259    =head3 EmergencyKey
1260    
1261        my $tkey = EmergencyKey($parameter);
1262    
1263    Return the Key to be used for emergency tracing. This could be an IP address,
1264     a session ID, or a user name, depending on the environment.
1265    
1266    =over 4
1267    
1268    =item parameter
1269    
1270    Parameter defining the method for finding the tracing key. If it is a scalar,
1271    then it is presumed to be the tracing key itself. If it is a CGI object, then
1272    the tracing key is taken from the C<IP> cookie. Otherwise, the tracing key is
1273    taken from the C<TRACING> environment variable.
1274    
1275    =item RETURN
1276    
1277    Returns the key to be used for labels in emergency tracing.
1278    
1279    =back
1280    
1281    =cut
1282    
1283    sub EmergencyKey {
1284        # Get the parameters.
1285        my ($parameter) = @_;
1286        # Declare the return variable.
1287        my $retVal;
1288        # Determine the parameter type.
1289        if (! defined $parameter || defined($ENV{TRACING})) {
1290            # Here we're supposed to check the environment. If that fails, we
1291            # get the effective login ID.
1292            $retVal = $ENV{TRACING} || scalar getpwuid($<);
1293        } else {
1294            my $ptype = ref $parameter;
1295            if ($ptype eq 'CGI') {
1296                # Here we were invoked from a web page. Look for a cookie.
1297                $retVal = $parameter->cookie('IP');
1298            } elsif (! $ptype) {
1299                # Here the key was passed in.
1300                $retVal = $parameter;
1301            }
1302        }
1303        # If no luck finding a key, use the PID.
1304        if (! defined $retVal) {
1305            $retVal = $$;
1306        }
1307        # Return the result.
1308        return $retVal;
1309    }
1310    
1311    
1312    =head3 TraceParms
1313    
1314        Tracer::TraceParms($cgi);
1315    
1316    Trace the CGI parameters at trace level CGI => 3 and the environment variables
1317    at level CGI => 4. A self-referencing URL is traced at level CGI => 2.
1318    
1319    =over 4
1320    
1321    =item cgi
1322    
1323    CGI query object containing the parameters to trace.
1324    
1325    =back
1326    
1327    =cut
1328    
1329    sub TraceParms {
1330        # Get the parameters.
1331        my ($cgi) = @_;
1332        if (T(CGI => 2)) {
1333            # Here we trace the GET-style URL for the script, but only if it's
1334            # relatively small.
1335            my $url = $cgi->url(-relative => 1, -query => 1);
1336            my $len = length($url);
1337            if ($len < 500) {
1338                Trace("[URL] $url");
1339            } elsif ($len > 2048) {
1340                Trace("[URL] URL is too long to use with GET ($len characters).");
1341            } else {
1342                Trace("[URL] URL length is $len characters.");
1343            }
1344        }
1345        if (T(CGI => 3)) {
1346            # Here we want to trace the parameter data.
1347            my @names = $cgi->param;
1348            for my $parmName (sort @names) {
1349                # Note we skip the Trace parameters, which are for our use only.
1350                if ($parmName ne 'Trace' && $parmName ne 'TF') {
1351                    my @values = $cgi->param($parmName);
1352                    Trace("[CGI] $parmName = " . join(", ", @values));
1353                }
1354            }
1355            # Display the request method.
1356            my $method = $cgi->request_method();
1357            Trace("Method: $method");
1358        }
1359        if (T(CGI => 4)) {
1360            # Here we want the environment data too.
1361            for my $envName (sort keys %ENV) {
1362                Trace("[ENV] $envName = $ENV{$envName}");
1363            }
1364        }
1365    }
1366    
1367    =head3 TraceImages
1368    
1369        Tracer::TraceImages($htmlString);
1370    
1371    Trace information about all of an html document's images. The tracing
1372    will be for type "IMG" at level 3. The image's source string
1373    will be displayed. This is generally either the URL of the image or
1374    raw data for the image itself. If the source is too long, only the first 300
1375    characters will be shown at trace level 3. The entire source will be shown,
1376    however, at trace level 4. This method is not very smart, and might catch
1377    Javascript code, but it is still useful when debugging the arcane
1378    behavior of images in multiple browser environments.
1379    
1380    =over 4
1381    
1382    =item htmlString
1383    
1384    HTML text for an outgoing web page.
1385    
1386    =back
1387    
1388    =cut
1389    
1390    sub TraceImages {
1391        # Only proceed if we're at the proper trace level.
1392        if (T(IMG => 3)) {
1393            # For performance reasons we're manipulating $_[0] instead of retrieving the string
1394            # into a variable called "$htmlString". This is because we expect html strings to be
1395            # long, and don't want to copy them any more than we have to.
1396            Trace(length($_[0]) . " characters in web page.");
1397            # Loop through the HTML, culling image tags.
1398            while ($_[0] =~ /<img\s+[^>]+?src="([^"]+)"/sgi) {
1399                # Extract the source string and determine whether or not it's too long.
1400                my $srcString = $1;
1401                my $pos = pos($_[0]) - length($srcString);
1402                my $excess = length($srcString) - 300;
1403                # We'll put the display string in here.
1404                my $srcDisplay = $srcString;
1405                # If it's a data string, split it at the comma.
1406                $srcDisplay =~ s/^(data[^,]+,)/$1\n/;
1407                # If there's no excess or we're at trace level 4, we're done. At level 3 with
1408                # a long string, however, we only show the first 300 characters.
1409                if ($excess > 0 && ! T(IMG => 4)) {
1410                    $srcDisplay = substr($srcDisplay,0,300) . "\nplus $excess characters.";
1411                }
1412                # Output the trace message.
1413                Trace("Image tag at position $pos:\n$srcDisplay");
1414            }
1415        }
1416    }
1417    
1418    =head2 Command-Line Utility Methods
1419    
1420    =head3 SendSMS
1421    
1422        my $msgID = Tracer::SendSMS($phoneNumber, $msg);
1423    
1424    Send a text message to a phone number using Clickatell. The FIG_Config file must contain the
1425    user name, password, and API ID for the relevant account in the hash reference variable
1426    I<$FIG_Config::phone>, using the keys C<user>, C<password>, and C<api_id>. For
1427    example, if the user name is C<BruceTheHumanPet>, the password is C<silly>, and the API ID
1428    is C<2561022>, then the FIG_Config file must contain
1429    
1430        $phone =  { user => 'BruceTheHumanPet',
1431                    password => 'silly',
1432                    api_id => '2561022' };
1433    
1434    The original purpose of this method was to insure Bruce would be notified immediately when the
1435    Sprout Load terminates. Care should be taken if you do not wish Bruce to be notified immediately
1436    when you call this method.
1437    
1438    The message ID will be returned if successful, and C<undef> if an error occurs.
1439    
1440    =over 4
1441    
1442    =item phoneNumber
1443    
1444    Phone number to receive the message, in international format. A United States phone number
1445    would be prefixed by "1". A British phone number would be prefixed by "44".
1446    
1447    =item msg
1448    
1449    Message to send to the specified phone.
1450    
1451    =item RETURN
1452    
1453    Returns the message ID if successful, and C<undef> if the message could not be sent.
1454    
1455    =back
1456    
1457    =cut
1458    
1459    sub SendSMS {
1460        # Get the parameters.
1461        my ($phoneNumber, $msg) = @_;
1462        # Declare the return variable. If we do not change it, C<undef> will be returned.
1463        my $retVal;
1464        # Only proceed if we have phone support.
1465        if (! defined $FIG_Config::phone) {
1466            Trace("Phone support not present in FIG_Config.") if T(1);
1467        } else {
1468            # Get the phone data.
1469            my $parms = $FIG_Config::phone;
1470            # Get the Clickatell URL.
1471            my $url = "http://api.clickatell.com/http/";
1472            # Create the user agent.
1473            my $ua = LWP::UserAgent->new;
1474            # Request a Clickatell session.
1475            my $resp = $ua->post("$url/sendmsg", { user => $parms->{user},
1476                                         password => $parms->{password},
1477                                         api_id => $parms->{api_id},
1478                                         to => $phoneNumber,
1479                                         text => $msg});
1480            # Check for an error.
1481            if (! $resp->is_success) {
1482                Trace("Alert failed.") if T(1);
1483            } else {
1484                # Get the message ID.
1485                my $rstring = $resp->content;
1486                if ($rstring =~ /^ID:\s+(.*)$/) {
1487                    $retVal = $1;
1488                } else {
1489                    Trace("Phone attempt failed with $rstring") if T(1);
1490                }
1491            }
1492        }
1493        # Return the result.
1494        return $retVal;
1495    }
1496    
1497    =head3 StandardSetup
1498    
1499        my ($options, @parameters) = StandardSetup(\@categories, \%options, $parmHelp, @ARGV);
1500    
1501    This method performs standard command-line parsing and tracing setup. The return
1502    values are a hash of the command-line options and a list of the positional
1503    parameters. Tracing is automatically set up and the command-line options are
1504    validated.
1505    
1506    This is a complex method that does a lot of grunt work. The parameters can
1507    be more easily understood, however, once they are examined individually.
1508    
1509    The I<categories> parameter is the most obtuse. It is a reference to a list of
1510    special-purpose tracing categories. Most tracing categories are PERL package
1511    names. So, for example, if you wanted to turn on tracing inside the B<Sprout>,
1512    B<ERDB>, and B<SproutLoad> packages, you would specify the categories
1513    
1514        ["Sprout", "SproutLoad", "ERDB"]
1515    
1516    This would cause trace messages in the specified three packages to appear in
1517    the output. There are two special tracing categories that are automatically
1518    handled by this method. In other words, if you used L</TSetup> you would need
1519    to include these categories manually, but if you use this method they are turned
1520    on automatically.
1521    
1522    =over 4
1523    
1524    =item SQL
1525    
1526    Traces SQL commands and activity.
1527    
1528    =item Tracer
1529    
1530    Traces error messages and call stacks.
1531    
1532    =back
1533    
1534    C<SQL> is only turned on if the C<-sql> option is specified in the command line.
1535    The trace level is specified using the C<-trace> command-line option. For example,
1536    the following command line for C<TransactFeatures> turns on SQL tracing and runs
1537    all tracing at level 3.
1538    
1539        TransactFeatures -trace=3 -sql register ../xacts IDs.tbl
1540    
1541    Standard tracing is output to the standard output and echoed to the file
1542    C<trace>I<$$>C<.log> in the FIG temporary directory, where I<$$> is the
1543    process ID. You can also specify the C<user> parameter to put a user ID
1544    instead of a process ID in the trace file name. So, for example
1545    
1546    The default trace level is 2. To get all messages, specify a trace level of 4.
1547    For a genome-by-genome update, use 3.
1548    
1549        TransactFeatures -trace=3 -sql -user=Bruce register ../xacts IDs.tbl
1550    
1551    would send the trace output to C<traceBruce.log> in the temporary directory.
1552    
1553    The I<options> parameter is a reference to a hash containing the command-line
1554    options, their default values, and an explanation of what they mean. Command-line
1555    options may be in the form of switches or keywords. In the case of a switch, the
1556    option value is 1 if it is specified and 0 if it is not specified. In the case
1557    of a keyword, the value is separated from the option name by an equal sign. You
1558    can see this last in the command-line example above.
1559    
1560    You can specify a different default trace level by setting C<$options->{trace}>
1561    prior to calling this method.
1562    
1563    An example at this point would help. Consider, for example, the command-line utility
1564    C<TransactFeatures>. It accepts a list of positional parameters plus the options
1565    C<safe>, C<noAlias>, C<start>, and C<tblFiles>. To start up this command, we execute
1566    the following code.
1567    
1568        my ($options, @parameters) = Tracer::StandardSetup(["DocUtils"],
1569                            { safe => [0, "use database transactions"],
1570                              noAlias => [0, "do not expect aliases in CHANGE transactions"],
1571                              start => [' ', "start with this genome"],
1572                              tblFiles => [0, "output TBL files containing the corrected IDs"] },
1573                            "<command> <transactionDirectory> <IDfile>",
1574                          @ARGV);
1575    
1576    
1577    The call to C<ParseCommand> specifies the default values for the options and
1578    stores the actual options in a hash that is returned as C<$options>. The
1579    positional parameters are returned in C<@parameters>.
1580    
1581    The following is a sample command line for C<TransactFeatures>.
1582    
1583        TransactFeatures -trace=2 -noAlias register ../xacts IDs.tbl
1584    
1585    Single and double hyphens are equivalent. So, you could also code the
1586    above command as
1587    
1588        TransactFeatures --trace=2 --noAlias register ../xacts IDs.tbl
1589    
1590    In this case, C<register>, C<../xacts>, and C<IDs.tbl> are the positional
1591    parameters, and would find themselves in I<@parameters> after executing the
1592    above code fragment. The tracing would be set to level 2, and the categories
1593    would be C<Tracer>, and <DocUtils>. C<Tracer> is standard,
1594    and C<DocUtils> was included because it came in within the first parameter
1595    to this method. The I<$options> hash would be
1596    
1597        { trace => 2, sql => 0, safe => 0,
1598          noAlias => 1, start => ' ', tblFiles => 0 }
1599    
1600    Use of C<StandardSetup> in this way provides a simple way of performing
1601    standard tracing setup and command-line parsing. Note that the caller is
1602    not even aware of the command-line switches C<-trace> and C<-sql>, which
1603    are used by this method to control the tracing. If additional tracing features
1604    need to be added in the future, they can be processed by this method without
1605    upsetting the command-line utilities.
1606    
1607    If the C<background> option is specified on the command line, then the
1608    standard and error outputs will be directed to files in the temporary
1609    directory, using the same suffix as the trace file. So, if the command
1610    line specified
1611    
1612        -user=Bruce -background
1613    
1614    then the trace output would go to C<traceBruce.log>, the standard output to
1615    C<outBruce.log>, and the error output to C<errBruce.log>. This is designed to
1616    simplify starting a command in the background.
1617    
1618    The user name is also used as the tracing key for L</Emergency Tracing>.
1619    Specifying a value of C<E> for the trace level causes emergency tracing to
1620    be used instead of custom tracing. If the user name is not specified,
1621    the tracing key is taken from the C<Tracing> environment variable. If there
1622    is no value for that variable, the tracing key will be computed from the active
1623    login ID.
1624    
1625    Since the default situation in StandardSetup is to trace to the standard
1626    output, errors that occur in command-line scripts will not generate
1627    RSS events. To force the events, use the C<warn> option.
1628    
1629        TransactFeatures -background -warn register ../xacts IDs.tbl
1630    
1631    Finally, if the special option C<-help> is specified, the option
1632    names will be traced at level 0 and the program will exit without processing.
1633    This provides a limited help capability. For example, if the user enters
1634    
1635        TransactFeatures -help
1636    
1637    he would see the following output.
1638    
1639        TransactFeatures [options] <command> <transactionDirectory> <IDfile>
1640            -trace    tracing level (default E)
1641            -sql      trace SQL commands
1642            -safe     use database transactions
1643            -noAlias  do not expect aliases in CHANGE transactions
1644            -start    start with this genome
1645            -tblFiles output TBL files containing the corrected IDs
1646            -forked   do not erase the trace file before tracing
1647    
1648    The caller has the option of modifying the tracing scheme by placing a value
1649    for C<trace> in the incoming options hash. The default value can be overridden,
1650    or the tracing to the standard output can be turned off by suffixing a minus
1651    sign to the trace level. So, for example,
1652    
1653        { trace => [0, "tracing level (default 0)"],
1654           ...
1655    
1656    would set the default trace level to 0 instead of E, while
1657    
1658        { trace => ["2-", "tracing level (default 2)"],
1659           ...
1660    
1661    would set the default to 2, but trace only to the log file, not to the
1662    standard output.
1663    
1664    The parameters to this method are as follows.
1665    
1666    =over 4
1667    
1668    =item categories
1669    
1670    Reference to a list of tracing category names. These should be names of
1671    packages whose internal workings will need to be debugged to get the
1672    command working.
1673    
1674    =item options
1675    
1676    Reference to a hash containing the legal options for the current command mapped
1677    to their default values and descriptions. The user can override the defaults
1678    by specifying the options as command-line switches prefixed by a hyphen.
1679    Tracing-related options may be added to this hash. If the C<-h> option is
1680    specified on the command line, the option descriptions will be used to
1681    explain the options. To turn off tracing to the standard output, add a
1682    minus sign to the value for C<trace> (see above).
1683    
1684    =item parmHelp
1685    
1686    A string that vaguely describes the positional parameters. This is used
1687    if the user specifies the C<-h> option.
1688    
1689    =item argv
1690    
1691    List of command line parameters, including the option switches, which must
1692    precede the positional parameters and be prefixed by a hyphen.
1693    
1694    =item RETURN
1695    
1696    Returns a list. The first element of the list is the reference to a hash that
1697    maps the command-line option switches to their values. These will either be the
1698    default values or overrides specified on the command line. The remaining
1699    elements of the list are the position parameters, in order.
1700    
1701    =back
1702    
1703    =cut
1704    
1705    sub StandardSetup {
1706        # Get the parameters.
1707        my ($categories, $options, $parmHelp, @argv) = @_;
1708        # Get the default tracing key.
1709        my $tkey = EmergencyKey();
1710        # Save the command line.
1711        $CommandLine = join(" ", $0, map { $_ =~ /\s/ ? "\"$_\"" : $_ } @argv);
1712        # Add the tracing options.
1713        if (! exists $options->{trace}) {
1714            $options->{trace} = ['2', "tracing level (E for emergency tracing)"];
1715        }
1716        if (! exists $options->{forked}) {
1717            $options->{forked} = [0, "keep old trace file"];
1718        }
1719        $options->{sql} = [0, "turn on SQL tracing"];
1720        $options->{help} = [0, "display command-line options"];
1721        $options->{user} = [$tkey, "tracing key"];
1722        $options->{background} = [0, "spool standard and error output"];
1723        $options->{warn} = [0, "send errors to RSS feed"];
1724        $options->{moreTracing} = ["", "comma-delimited list of additional trace modules for debugging"];
1725        # Create a parsing hash from the options hash. The parsing hash
1726        # contains the default values rather than the default value
1727        # and the description. While we're at it, we'll memorize the
1728        # length of the longest option name.
1729        my $longestName = 0;
1730        my %parseOptions = ();
1731        for my $key (keys %{$options}) {
1732            if (length $key > $longestName) {
1733                $longestName = length $key;
1734            }
1735            $parseOptions{$key} = $options->{$key}->[0];
1736        }
1737        # Parse the command line.
1738        my ($retOptions, @retParameters) = ParseCommand(\%parseOptions, @argv);
1739        # Get the logfile suffix.
1740        my $suffix = $retOptions->{user};
1741        # We'll put the trace file name in here. We need it later if background
1742        # mode is on.
1743        my $traceFileName;
1744        # Now we want to set up tracing. First, we need to know if the user
1745        # wants emergency tracing.
1746        if ($retOptions->{trace} eq 'E') {
1747            ETracing($retOptions->{user});
1748        } else {
1749            # Here the tracing is controlled from the command line.
1750            my @cats = @{$categories};
1751            if ($retOptions->{sql}) {
1752                push @cats, "SQL";
1753            }
1754            if ($retOptions->{warn}) {
1755                push @cats, "Feed";
1756            }
1757            # Add the default categories.
1758            push @cats, "Tracer";
1759            # Check for more tracing groups.
1760            if ($retOptions->{moreTracing}) {
1761                push @cats, split /,/, $retOptions->{moreTracing};
1762            }
1763            # Next, we create the category string by joining the categories.
1764            my $cats = join(" ", @cats);
1765            # Check to determine whether or not the caller wants to turn off tracing
1766            # to the standard output.
1767            my $traceLevel = $retOptions->{trace};
1768            my $textOKFlag = 1;
1769            if ($traceLevel =~ /^(.)-/) {
1770                $traceLevel = $1;
1771                $textOKFlag = 0;
1772            }
1773            # Now we set up the trace mode.
1774            my $traceMode;
1775            # Verify that we can open a file in the FIG temporary directory.
1776            my $traceFileName = "$FIG_Config::temp/trace$suffix.log";
1777            my $traceFileSpec = ($retOptions->{forked} ? ">>$traceFileName" : ">$traceFileName");
1778            if (open TESTTRACE, "$traceFileSpec") {
1779                # Here we can trace to a file.
1780                $traceMode = ">>$traceFileName";
1781                if ($textOKFlag) {
1782                    # Echo to standard output if the text-OK flag is set.
1783                    $traceMode = "+$traceMode";
1784                }
1785                # Close the test file.
1786                close TESTTRACE;
1787            } else {
1788                # Here we can't trace to a file. Complain about this.
1789                warn "Could not open trace file $traceFileName: $!\n";
1790                # We trace to the standard output if it's
1791                # okay, and the error log otherwise.
1792                if ($textOKFlag) {
1793                    $traceMode = "TEXT";
1794                } else {
1795                    $traceMode = "WARN";
1796                }
1797            }
1798            # Now set up the tracing.
1799            TSetup("$traceLevel $cats", $traceMode);
1800        }
1801        # Check for background mode.
1802        if ($retOptions->{background}) {
1803            my $outFileName = "$FIG_Config::temp/out$suffix$$.log";
1804            my $errFileName = "$FIG_Config::temp/err$suffix$$.log";
1805            # Spool the output.
1806            open STDOUT, ">$outFileName";
1807            # If we have a trace file, trace the errors to the log. Otherwise,
1808            # spool the errors.
1809            if (defined $traceFileName) {
1810                open STDERR, "| Tracer $traceFileName";
1811            } else {
1812                open STDERR, ">$errFileName";
1813            }
1814            # Check for phone support. If we have phone support and a phone number,
1815            # we want to turn it on.
1816            if ($ENV{PHONE} && defined($FIG_Config::phone)) {
1817                $retOptions->{phone} = $ENV{PHONE};
1818            }
1819        }
1820        # Check for the "help" option. If it is specified, dump the command-line
1821        # options and exit the program.
1822        if ($retOptions->{help}) {
1823            $0 =~ m#[/\\](\w+)(\.pl)?$#i;
1824            print "$1 [options] $parmHelp\n";
1825            for my $key (sort keys %{$options}) {
1826                my $name = Pad($key, $longestName, 0, ' ');
1827                my $desc = $options->{$key}->[1];
1828                if ($options->{$key}->[0]) {
1829                    $desc .= " (default " . $options->{$key}->[0] . ")";
1830                }
1831                print "  $name $desc\n";
1832            }
1833            exit(0);
1834        }
1835        # Trace the options, if applicable.
1836        if (T(3)) {
1837            my @parms = grep { $retOptions->{$_} } keys %{$retOptions};
1838            Trace("Selected options: " . join(", ", sort @parms) . ".");
1839        }
1840        # Return the parsed parameters.
1841        return ($retOptions, @retParameters);
1842    }
1843    
1844    =head3 ReadOptions
1845    
1846        my %options = Tracer::ReadOptions($fileName);
1847    
1848    Read a set of options from a file. Each option is encoded in a line of text that has the
1849    format
1850    
1851    I<optionName>C<=>I<optionValue>C<; >I<comment>
1852    
1853    The option name must consist entirely of letters, digits, and the punctuation characters
1854    C<.> and C<_>, and is case sensitive. Blank lines and lines in which the first nonblank
1855    character is a semi-colon will be ignored. The return hash will map each option name to
1856    the corresponding option value.
1857    
1858    =over 4
1859    
1860    =item fileName
1861    
1862    Name of the file containing the option data.
1863    
1864    =item RETURN
1865    
1866    Returns a hash mapping the option names specified in the file to their corresponding option
1867    value.
1868    
1869    =back
1870    
1871    =cut
1872    
1873    sub ReadOptions {
1874        # Get the parameters.
1875        my ($fileName) = @_;
1876        # Open the file.
1877        (open CONFIGFILE, "<$fileName") || Confess("Could not open option file $fileName.");
1878        # Count the number of records read.
1879        my ($records, $comments) = 0;
1880        # Create the return hash.
1881        my %retVal = ();
1882        # Loop through the file, accumulating key-value pairs.
1883        while (my $line = <CONFIGFILE>) {
1884            # Denote we've read a line.
1885            $records++;
1886            # Determine the line type.
1887            if ($line =~ /^\s*[\n\r]/) {
1888                # A blank line is a comment.
1889                $comments++;
1890            } elsif ($line =~ /^\s*([A-Za-z0-9_\.]+)=([^;]*);/) {
1891                # Here we have an option assignment.
1892                retVal{$1} = $2;
1893            } elsif ($line =~ /^\s*;/) {
1894                # Here we have a text comment.
1895                $comments++;
1896            } else {
1897                # Here we have an invalid line.
1898                Trace("Invalid option statement in record $records.") if T(0);
1899            }
1900        }
1901        # Return the hash created.
1902        return %retVal;
1903    }
1904    
1905    =head3 GetOptions
1906    
1907        Tracer::GetOptions(\%defaults, \%options);
1908    
1909    Merge a specified set of options into a table of defaults. This method takes two hash references
1910    as input and uses the data from the second to update the first. If the second does not exist,
1911    there will be no effect. An error will be thrown if one of the entries in the second hash does not
1912    exist in the first.
1913    
1914    Consider the following example.
1915    
1916        my $optionTable = GetOptions({ dbType => 'mySQL', trace => 0 }, $options);
1917    
1918    In this example, the variable B<$options> is expected to contain at most two options-- B<dbType> and
1919    B<trace>. The default database type is C<mySQL> and the default trace level is C<0>. If the value of
1920    B<$options> is C<< {dbType => 'Oracle'} >>, then the database type will be changed to C<Oracle> and
1921    the trace level will remain at 0. If B<$options> is undefined, then the database type and trace level
1922    will remain C<mySQL> and C<0>. If, on the other hand, B<$options> is defined as
1923    
1924        {databaseType => 'Oracle'}
1925    
1926    an error will occur because the B<databaseType> option does not exist.
1927    
1928    =over 4
1929    
1930    =item defaults
1931    
1932    Table of default option values.
1933    
1934    =item options
1935    
1936    Table of overrides, if any.
1937    
1938    =item RETURN
1939    
1940    Returns a reference to the default table passed in as the first parameter.
1941    
1942    =back
1943    
1944    =cut
1945    
1946    sub GetOptions {
1947        # Get the parameters.
1948        my ($defaults, $options) = @_;
1949        # Check for overrides.
1950        if ($options) {
1951            # Loop through the overrides.
1952            while (my ($option, $setting) = each %{$options}) {
1953                # Insure this override exists.
1954                if (!exists $defaults->{$option}) {
1955                    croak "Unrecognized option $option encountered.";
1956                } else {
1957                    # Apply the override.
1958                    $defaults->{$option} = $setting;
1959                }
1960            }
1961        }
1962        # Return the merged table.
1963        return $defaults;
1964    }
1965    
1966    =head3 MergeOptions
1967    
1968        Tracer::MergeOptions(\%table, \%defaults);
1969    
1970    Merge default values into a hash table. This method looks at the key-value pairs in the
1971    second (default) hash, and if a matching key is not found in the first hash, the default
1972    pair is copied in. The process is similar to L</GetOptions>, but there is no error-
1973    checking and no return value.
1974    
1975    =over 4
1976    
1977    =item table
1978    
1979    Hash table to be updated with the default values.
1980    
1981    =item defaults
1982    
1983    Default values to be merged into the first hash table if they are not already present.
1984    
1985    =back
1986    
1987    =cut
1988    
1989    sub MergeOptions {
1990        # Get the parameters.
1991        my ($table, $defaults) = @_;
1992        # Loop through the defaults.
1993        while (my ($key, $value) = each %{$defaults}) {
1994            if (!exists $table->{$key}) {
1995                $table->{$key} = $value;
1996            }
1997        }
1998    }
1999    
2000    =head3 UnparseOptions
2001    
2002        my $optionString = Tracer::UnparseOptions(\%options);
2003    
2004    Convert an option hash into a command-line string. This will not
2005    necessarily be the same text that came in, but it will nonetheless
2006    produce the same ultimate result when parsed by L</StandardSetup>.
2007    
2008    =over 4
2009    
2010    =item options
2011    
2012    Reference to a hash of options to convert into an option string.
2013    
2014    =item RETURN
2015    
2016    Returns a string that will parse to the same set of options when
2017    parsed by L</StandardSetup>.
2018    
2019    =back
2020    
2021    =cut
2022    
2023    sub UnparseOptions {
2024        # Get the parameters.
2025        my ($options) = @_;
2026        # The option segments will be put in here.
2027        my @retVal = ();
2028        # Loop through the options.
2029        for my $key (keys %$options) {
2030            # Get the option value.
2031            my $value = $options->{$key};
2032            # Only use it if it's nonempty.
2033            if (defined $value && $value ne "") {
2034                my $segment = "--$key=$value";
2035                # Quote it if necessary.
2036                if ($segment =~ /[ |<>*]/) {
2037                    $segment = '"' . $segment . '"';
2038                }
2039                # Add it to the return list.
2040                push @retVal, $segment;
2041            }
2042        }
2043        # Return the result.
2044        return join(" ", @retVal);
2045    }
2046    
2047    =head3 ParseCommand
2048    
2049        my ($options, @arguments) = Tracer::ParseCommand(\%optionTable, @inputList);
2050    
2051    Parse a command line consisting of a list of parameters. The initial parameters may be option
2052    specifiers of the form C<->I<option> or C<->I<option>C<=>I<value>. The options are stripped
2053    off and merged into a table of default options. The remainder of the command line is
2054    returned as a list of positional arguments. For example, consider the following invocation.
2055    
2056        my ($options, @arguments) = ParseCommand({ errors => 0, logFile => 'trace.log'}, @words);
2057    
2058    In this case, the list @words will be treated as a command line and there are two options available,
2059    B<errors> and B<logFile>. If @words has the following format
2060    
2061        -logFile=error.log apple orange rutabaga
2062    
2063    then at the end of the invocation, C<$options> will be
2064    
2065        { errors => 0, logFile => 'error.log' }
2066    
2067    and C<@arguments> will contain
2068    
2069        apple orange rutabaga
2070    
2071    The parser allows for some escape sequences. See L</UnEscape> for a description. There is no
2072    support for quote characters. Options can be specified with single or double hyphens.
2073    
2074    =over 4
2075    
2076    =item optionTable
2077    
2078    Table of default options.
2079    
2080    =item inputList
2081    
2082    List of words on the command line.
2083    
2084    =item RETURN
2085    
2086    Returns a reference to the option table and a list of the positional arguments.
2087    
2088    =back
2089    
2090    =cut
2091    
2092    sub ParseCommand {
2093        # Get the parameters.
2094        my ($optionTable, @inputList) = @_;
2095        # Process any options in the input list.
2096        my %overrides = ();
2097        while ((@inputList > 0) && ($inputList[0] =~ /^--?/)) {
2098            # Get the current option.
2099            my $arg = shift @inputList;
2100            # Pull out the option name.
2101            $arg =~ /^--?([^=]*)/g;
2102            my $name = $1;
2103            # Check for an option value.
2104            if ($arg =~ /\G=(.*)$/g) {
2105                # Here we have a value for the option.
2106                $overrides{$name} = UnEscape($1);
2107            } else {
2108                # Here there is no value, so we use 1.
2109                $overrides{$name} = 1;
2110            }
2111        }
2112        # Merge the options into the defaults.
2113        GetOptions($optionTable, \%overrides);
2114        # Translate the remaining parameters.
2115        my @retVal = ();
2116        for my $inputParm (@inputList) {
2117            push @retVal, UnEscape($inputParm);
2118        }
2119        # Return the results.
2120        return ($optionTable, @retVal);
2121    }
2122    
2123    
2124    =head2 File Utility Methods
2125    
2126    =head3 GetFile
2127    
2128        my @fileContents = Tracer::GetFile($fileName);
2129    
2130        or
2131    
2132        my $fileContents = Tracer::GetFile($fileName);
2133    
2134    Return the entire contents of a file. In list context, line-ends are removed and
2135    each line is a list element. In scalar context, line-ends are replaced by C<\n>.
2136    
2137    =over 4
2138    
2139    =item fileName
2140    
2141    Name of the file to read.
2142    
2143    =item RETURN
2144    
2145    In a list context, returns the entire file as a list with the line terminators removed.
2146    In a scalar context, returns the entire file as a string. If an error occurs opening
2147    the file, an empty list will be returned.
2148    
2149    =back
2150    
2151    =cut
2152    
2153    sub GetFile {
2154        # Get the parameters.
2155        my ($fileName) = @_;
2156        # Declare the return variable.
2157        my @retVal = ();
2158        # Open the file for input.
2159        my $handle = Open(undef, "<$fileName");
2160        # Read the whole file into the return variable, stripping off any terminator
2161        # characters.
2162        my $lineCount = 0;
2163        while (my $line = <$handle>) {
2164            $lineCount++;
2165            $line = Strip($line);
2166            push @retVal, $line;
2167        }
2168        # Close it.
2169        close $handle;
2170        my $actualLines = @retVal;
2171        Trace("$actualLines lines read from file $fileName.") if T(File => 2);
2172        # Return the file's contents in the desired format.
2173        if (wantarray) {
2174            return @retVal;
2175        } else {
2176            return join "\n", @retVal;
2177        }
2178    }
2179    
2180    =head3 PutFile
2181    
2182        Tracer::PutFile($fileName, \@lines);
2183    
2184    Write out a file from a list of lines of text.
2185    
2186    =over 4
2187    
2188    =item fileName
2189    
2190    Name of the output file.
2191    
2192    =item lines
2193    
2194    Reference to a list of text lines. The lines will be written to the file in order, with trailing
2195    new-line characters. Alternatively, may be a string, in which case the string will be written without
2196    modification.
2197    
2198    =back
2199    
2200    =cut
2201    
2202    sub PutFile {
2203        # Get the parameters.
2204        my ($fileName, $lines) = @_;
2205        # Open the output file.
2206        my $handle = Open(undef, ">$fileName");
2207        # Count the lines written.
2208        if (ref $lines ne 'ARRAY') {
2209            # Here we have a scalar, so we write it raw.
2210            print $handle $lines;
2211            Trace("Scalar put to file $fileName.") if T(File => 3);
2212        } else {
2213            # Write the lines one at a time.
2214            my $count = 0;
2215            for my $line (@{$lines}) {
2216                print $handle "$line\n";
2217                $count++;
2218            }
2219            Trace("$count lines put to file $fileName.") if T(File => 3);
2220        }
2221        # Close the output file.
2222        close $handle;
2223    }
2224    
2225    =head3 ParseRecord
2226    
2227        my @fields = Tracer::ParseRecord($line);
2228    
2229    Parse a tab-delimited data line. The data line is split into field values. Embedded tab
2230    and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.
2231    These will automatically be converted.
2232    
2233    =over 4
2234    
2235    =item line
2236    
2237    Line of data containing the tab-delimited fields.
2238    
2239    =item RETURN
2240    
2241    Returns a list of the fields found in the data line.
2242    
2243    =back
2244    
2245    =cut
2246    
2247    sub ParseRecord {
2248        # Get the parameter.
2249        my ($line) = @_;
2250        # Remove the trailing new-line, if any.
2251        chomp $line;
2252        # Split the line read into pieces using the tab character.
2253        my @retVal = split /\t/, $line;
2254        # Trim and fix the escapes in each piece.
2255        for my $value (@retVal) {
2256            # Trim leading whitespace.
2257            $value =~ s/^\s+//;
2258            # Trim trailing whitespace.
2259            $value =~ s/\s+$//;
2260            # Delete the carriage returns.
2261            $value =~ s/\r//g;
2262            # Convert the escapes into their real values.
2263            $value =~ s/\\t/"\t"/ge;
2264            $value =~ s/\\n/"\n"/ge;
2265        }
2266        # Return the result.
2267        return @retVal;
2268    }
2269    
2270    =head3 Merge
2271    
2272        my @mergedList = Tracer::Merge(@inputList);
2273    
2274    Sort a list of strings and remove duplicates.
2275    
2276    =over 4
2277    
2278    =item inputList
2279    
2280    List of scalars to sort and merge.
2281    
2282    =item RETURN
2283    
2284    Returns a list containing the same elements sorted in ascending order with duplicates
2285    removed.
2286    
2287    =back
2288    
2289    =cut
2290    
2291    sub Merge {
2292        # Get the input list in sort order.
2293        my @inputList = sort @_;
2294        # Only proceed if the list has at least two elements.
2295        if (@inputList > 1) {
2296            # Now we want to move through the list splicing out duplicates.
2297            my $i = 0;
2298            while ($i < @inputList) {
2299                # Get the current entry.
2300                my $thisEntry = $inputList[$i];
2301                # Find out how many elements duplicate the current entry.
2302                my $j = $i + 1;
2303                my $dup1 = $i + 1;
2304                while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };
2305                # If the number is nonzero, splice out the duplicates found.
2306                if ($j > $dup1) {
2307                    splice @inputList, $dup1, $j - $dup1;
2308                }
2309                # Now the element at position $dup1 is different from the element before it
2310                # at position $i. We push $i forward one position and start again.
2311                $i++;
2312            }
2313        }
2314        # Return the merged list.
2315        return @inputList;
2316    }
2317    
2318    =head3 Open
2319    
2320        my $handle = Open($fileHandle, $fileSpec, $message);
2321    
2322    Open a file.
2323    
2324    The I<$fileSpec> is essentially the second argument of the PERL C<open>
2325    function. The mode is specified using Unix-like shell information. So, for
2326    example,
2327    
2328        Open(\*LOGFILE, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2329    
2330    would open for output appended to the specified file, and
2331    
2332        Open(\*DATASTREAM, "| sort -u >$outputFile", "Could not open $outputFile.");
2333    
2334    would open a pipe that sorts the records written and removes duplicates. Note
2335    the use of file handle syntax in the Open call. To use anonymous file handles,
2336    code as follows.
2337    
2338        my $logFile = Open(undef, '>>/usr/spool/news/twitlog', "Could not open twit log.");
2339    
2340    The I<$message> parameter is used if the open fails. If it is set to C<0>, then
2341    the open returns TRUE if successful and FALSE if an error occurred. Otherwise, a
2342    failed open will throw an exception and the third parameter will be used to construct
2343    an error message. If the parameter is omitted, a standard message is constructed
2344    using the file spec.
2345    
2346        Could not open "/usr/spool/news/twitlog"
2347    
2348    Note that the mode characters are automatically cleaned from the file name.
2349    The actual error message from the file system will be captured and appended to the
2350    message in any case.
2351    
2352        Could not open "/usr/spool/news/twitlog": file not found.
2353    
2354    In some versions of PERL the only error message we get is a number, which
2355    corresponds to the C++ C<errno> value.
2356    
2357        Could not open "/usr/spool/news/twitlog": 6.
2358    
2359    =over 4
2360    
2361    =item fileHandle
2362    
2363    File handle. If this parameter is C<undef>, a file handle will be generated
2364    and returned as the value of this method.
2365    
2366    =item fileSpec
2367    
2368    File name and mode, as per the PERL C<open> function.
2369    
2370    =item message (optional)
2371    
2372    Error message to use if the open fails. If omitted, a standard error message
2373    will be generated. In either case, the error information from the file system
2374    is appended to the message. To specify a conditional open that does not throw
2375    an error if it fails, use C<0>.
2376    
2377    =item RETURN
2378    
2379    Returns the name of the file handle assigned to the file, or C<undef> if the
2380    open failed.
2381    
2382    =back
2383    
2384    =cut
2385    
2386    sub Open {
2387        # Get the parameters.
2388        my ($fileHandle, $fileSpec, $message) = @_;
2389        # Attempt to open the file.
2390        my $rv = open $fileHandle, $fileSpec;
2391        # If the open failed, generate an error message.
2392        if (! $rv) {
2393            # Save the system error message.
2394            my $sysMessage = $!;
2395            # See if we need a default message.
2396            if (!$message) {
2397                # Clean any obvious mode characters and leading spaces from the
2398                # filename.
2399                my ($fileName) = FindNamePart($fileSpec);
2400                $message = "Could not open \"$fileName\"";
2401            }
2402            # Terminate with an error using the supplied message and the
2403            # error message from the file system.
2404            Confess("$message: $!");
2405        }
2406        # Return the file handle.
2407        return $fileHandle;
2408    }
2409    
2410    =head3 FindNamePart
2411    
2412        my ($fileName, $start, $len) = Tracer::FindNamePart($fileSpec);
2413    
2414    Extract the portion of a file specification that contains the file name.
2415    
2416    A file specification is the string passed to an C<open> call. It specifies the file
2417    mode and name. In a truly complex situation, it can specify a pipe sequence. This
2418    method assumes that the file name is whatever follows the first angle bracket
2419    sequence.  So, for example, in the following strings the file name is
2420    C</usr/fig/myfile.txt>.
2421    
2422        >>/usr/fig/myfile.txt
2423        </usr/fig/myfile.txt
2424        | sort -u > /usr/fig/myfile.txt
2425    
2426    If the method cannot find a file name using its normal methods, it will return the
2427    whole incoming string.
2428    
2429    =over 4
2430    
2431    =item fileSpec
2432    
2433    File specification string from which the file name is to be extracted.
2434    
2435    =item RETURN
2436    
2437    Returns a three-element list. The first element contains the file name portion of
2438    the specified string, or the whole string if a file name cannot be found via normal
2439    methods. The second element contains the start position of the file name portion and
2440    the third element contains the length.
2441    
2442    =back
2443    
2444    =cut
2445    #: Return Type $;
2446    sub FindNamePart {
2447        # Get the parameters.
2448        my ($fileSpec) = @_;
2449        # Default to the whole input string.
2450        my ($retVal, $pos, $len) = ($fileSpec, 0, length $fileSpec);
2451        # Parse out the file name if we can.
2452        if ($fileSpec =~ m/(<|>>?)(.+?)(\s*)$/) {
2453            $retVal = $2;
2454            $len = length $retVal;
2455            $pos = (length $fileSpec) - (length $3) - $len;
2456        }
2457        # Return the result.
2458        return ($retVal, $pos, $len);
2459    }
2460    
2461    =head3 OpenDir
2462    
2463        my @files = OpenDir($dirName, $filtered, $flag);
2464    
2465    Open a directory and return all the file names. This function essentially performs
2466    the functions of an C<opendir> and C<readdir>. If the I<$filtered> parameter is
2467    set to TRUE, all filenames beginning with a period (C<.>), dollar sign (C<$>),
2468    or pound sign (C<#>) and all filenames ending with a tilde C<~>) will be
2469    filtered out of the return list. If the directory does not open and I<$flag> is not
2470    set, an exception is thrown. So, for example,
2471    
2472        my @files = OpenDir("/Volumes/fig/contigs", 1);
2473    
2474    is effectively the same as
2475    
2476        opendir(TMP, "/Volumes/fig/contigs") || Confess("Could not open /Volumes/fig/contigs.");
2477        my @files = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir(TMP);
2478    
2479    Similarly, the following code
2480    
2481        my @files = grep { $_ =~ /^\d/ } OpenDir("/Volumes/fig/orgs", 0, 1);
2482    
2483    Returns the names of all files in C</Volumes/fig/orgs> that begin with digits and
2484    automatically returns an empty list if the directory fails to open.
2485    
2486    =over 4
2487    
2488    =item dirName
2489    
2490    Name of the directory to open.
2491    
2492    =item filtered
2493    
2494    TRUE if files whose names begin with a period (C<.>) should be automatically removed
2495    from the list, else FALSE.
2496    
2497    =item flag
2498    
2499    TRUE if a failure to open is okay, else FALSE
2500    
2501    =back
2502    
2503    =cut
2504    #: Return Type @;
2505    sub OpenDir {
2506        # Get the parameters.
2507        my ($dirName, $filtered, $flag) = @_;
2508        # Declare the return variable.
2509        my @retVal = ();
2510        # Open the directory.
2511        if (opendir(my $dirHandle, $dirName)) {
2512            # The directory opened successfully. Get the appropriate list according to the
2513            # strictures of the filter parameter.
2514            if ($filtered) {
2515                @retVal = grep { $_ !~ /^[\.\$\#]/ && $_ !~ /~$/ } readdir $dirHandle;
2516            } else {
2517                @retVal = readdir $dirHandle;
2518            }
2519        } elsif (! $flag) {
2520            # Here the directory would not open and it's considered an error.
2521            Confess("Could not open directory $dirName.");
2522        }
2523        # Return the result.
2524        return @retVal;
2525    }
2526    
2527    
2528    =head3 Insure
2529    
2530        Insure($dirName, $chmod);
2531    
2532    Insure a directory is present.
2533    
2534    =over 4
2535    
2536    =item dirName
2537    
2538    Name of the directory to check. If it does not exist, it will be created.
2539    
2540    =item chmod (optional)
2541    
2542    Security privileges to be given to the directory if it is created.
2543    
2544    =back
2545    
2546    =cut
2547    
2548    sub Insure {
2549        my ($dirName, $chmod) = @_;
2550        if (! -d $dirName) {
2551            Trace("Creating $dirName directory.") if T(2);
2552            eval {
2553                mkpath $dirName;
2554                # If we have permissions specified, set them here.
2555                if (defined($chmod)) {
2556                    chmod $chmod, $dirName;
2557                }
2558            };
2559            if ($@) {
2560                Confess("Error creating $dirName: $@");
2561            }
2562        }
2563    }
2564    
2565    =head3 ChDir
2566    
2567        ChDir($dirName);
2568    
2569    Change to the specified directory.
2570    
2571    =over 4
2572    
2573    =item dirName
2574    
2575    Name of the directory to which we want to change.
2576    
2577    =back
2578    
2579    =cut
2580    
2581    sub ChDir {
2582        my ($dirName) = @_;
2583        if (! -d $dirName) {
2584            Confess("Cannot change to directory $dirName: no such directory.");
2585        } else {
2586            Trace("Changing to directory $dirName.") if T(File => 4);
2587            my $okFlag = chdir $dirName;
2588            if (! $okFlag) {
2589                Confess("Error switching to directory $dirName.");
2590            }
2591        }
2592    }
2593    
2594    =head3 SetPermissions
2595    
2596        Tracer::SetPermissions($dirName, $group, $mask, %otherMasks);
2597    
2598    Set the permissions for a directory and all the files and folders inside it.
2599    In addition, the group ownership will be changed to the specified value.
2600    
2601    This method is more vulnerable than most to permission and compatability
2602    problems, so it does internal error recovery.
2603    
2604    =over 4
2605    
2606    =item dirName
2607    
2608    Name of the directory to process.
2609    
2610    =item group
2611    
2612    Name of the group to be assigned.
2613    
2614    =item mask
2615    
2616    Permission mask. Bits that are C<1> in this mask will be ORed into the
2617    permission bits of any file or directory that does not already have them
2618    set to 1.
2619    
2620    =item otherMasks
2621    
2622    Map of search patterns to permission masks. If a directory name matches
2623    one of the patterns, that directory and all its members and subdirectories
2624    will be assigned the new pattern. For example, the following would
2625    assign 0664 to most files, but would use 0777 for directories named C<tmp>.
2626    
2627        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp$' => 01777);
2628    
2629    The list is ordered, so the following would use 0777 for C<tmp1> and
2630    0666 for C<tmp>, C<tmp2>, or C<tmp3>.
2631    
2632        Tracer::SetPermissions($dirName, 'fig', 01664, '^tmp1' => 0777,
2633                                                       '^tmp' => 0666);
2634    
2635    Note that the pattern matches are all case-insensitive, and only directory
2636    names are matched, not file names.
2637    
2638    =back
2639    
2640    =cut
2641    
2642    sub SetPermissions {
2643        # Get the parameters.
2644        my ($dirName, $group, $mask, @otherMasks) = @_;
2645        # Set up for error recovery.
2646        eval {
2647            # Switch to the specified directory.
2648            ChDir($dirName);
2649            # Get the group ID.
2650            my $gid = getgrnam($group);
2651            # Get the mask for tracing.
2652            my $traceMask = sprintf("%04o", $mask) . "($mask)";
2653            Trace("Fixing permissions for directory $dirName using group $group($gid) and mask $traceMask.") if T(File => 2);
2654            my $fixCount = 0;
2655            my $lookCount = 0;
2656            # @dirs will be a stack of directories to be processed.
2657            my @dirs = (getcwd());
2658            while (scalar(@dirs) > 0) {
2659                # Get the current directory.
2660                my $dir = pop @dirs;
2661                # Check for a match to one of the specified directory names. To do
2662                # that, we need to pull the individual part of the name off of the
2663                # whole path.
2664                my $simpleName = $dir;
2665                if ($dir =~ m!/([^/]+)$!) {
2666                    $simpleName = $1;
2667                }
2668                Trace("Simple directory name for $dir is $simpleName.") if T(File => 4);
2669                # Search for a match.
2670                my $match = 0;
2671                my $i;
2672                for ($i = 0; $i < $#otherMasks && ! $match; $i += 2) {
2673                    my $pattern = $otherMasks[$i];
2674                    if ($simpleName =~ /$pattern/i) {
2675                        $match = 1;
2676                    }
2677                }
2678                # Find out if we have a match. Note we use $i-1 because the loop added 2
2679                # before terminating due to the match.
2680                if ($match && $otherMasks[$i-1] != $mask) {
2681                    # This directory matches one of the incoming patterns, and it's
2682                    # a different mask, so we process it recursively with that mask.
2683                    SetPermissions($dir, $group, $otherMasks[$i-1], @otherMasks);
2684                } else {
2685                    # Here we can process normally. Get all of the non-hidden members.
2686                    my @submems = OpenDir($dir, 1);
2687                    for my $submem (@submems) {
2688                        # Get the full name.
2689                        my $thisMem = "$dir/$submem";
2690                        Trace("Checking member $thisMem.") if T(4);
2691                        $lookCount++;
2692                        if ($lookCount % 1000 == 0) {
2693                            Trace("$lookCount members examined. Current is $thisMem. Mask is $traceMask") if T(File => 3);
2694                        }
2695                        # Fix the group.
2696                        chown -1, $gid, $thisMem;
2697                        # Insure this member is not a symlink.
2698                        if (! -l $thisMem) {
2699                            # Get its info.
2700                            my $fileInfo = stat $thisMem;
2701                            # Only proceed if we got the info. Otherwise, it's a hard link
2702                            # and we want to skip it anyway.
2703                            if ($fileInfo) {
2704                                my $fileMode = $fileInfo->mode;
2705                                if (($fileMode & $mask) != $mask) {
2706                                    # Fix this member.
2707                                    $fileMode |= $mask;
2708                                    chmod $fileMode, $thisMem;
2709                                    $fixCount++;
2710                                }
2711                                # If it's a subdirectory, stack it.
2712                                if (-d $thisMem) {
2713                                    push @dirs, $thisMem;
2714                                }
2715                            }
2716                        }
2717                    }
2718                }
2719            }
2720            Trace("$lookCount files and directories processed, $fixCount fixed.") if T(File => 2);
2721        };
2722        # Check for an error.
2723        if ($@) {
2724            Confess("SetPermissions error: $@");
2725        }
2726    }
2727    
2728    =head3 GetLine
2729    
2730        my @data = Tracer::GetLine($handle);
2731    
2732    Read a line of data from a tab-delimited file.
2733    
2734    =over 4
2735    
2736    =item handle
2737    
2738    Open file handle from which to read.
2739    
2740    =item RETURN
2741    
2742    Returns a list of the fields in the record read. The fields are presumed to be
2743    tab-delimited. If we are at the end of the file, then an empty list will be
2744    returned. If an empty line is read, a single list item consisting of a null
2745    string will be returned.
2746    
2747    =back
2748    
2749    =cut
2750    
2751    sub GetLine {
2752        # Get the parameters.
2753        my ($handle) = @_;
2754        # Declare the return variable.
2755        my @retVal = ();
2756        Trace("File position is " . tell($handle) . ". EOF flag is " . eof($handle) . ".") if T(File => 4);
2757        # Read from the file.
2758        my $line = <$handle>;
2759        # Only proceed if we found something.
2760        if (defined $line) {
2761            # Remove the new-line. We are a bit over-cautious here because the file may be coming in via an
2762            # upload control and have a nonstandard EOL combination.
2763            $line =~ s/(\r|\n)+$//;
2764            # Here we do some fancy tracing to help in debugging complicated EOL marks.
2765            if (T(File => 4)) {
2766                my $escapedLine = $line;
2767                $escapedLine =~ s/\n/\\n/g;
2768                $escapedLine =~ s/\r/\\r/g;
2769                $escapedLine =~ s/\t/\\t/g;
2770                Trace("Line read: -->$escapedLine<--");
2771            }
2772            # If the line is empty, return a single empty string; otherwise, parse
2773            # it into fields.
2774            if ($line eq "") {
2775                push @retVal, "";
2776            } else {
2777                push @retVal, split /\t/,$line;
2778            }
2779        } else {
2780            # Trace the reason the read failed.
2781            Trace("End of file: $!") if T(File => 3);
2782        }
2783        # Return the result.
2784        return @retVal;
2785    }
2786    
2787    =head3 PutLine
2788    
2789        Tracer::PutLine($handle, \@fields, $eol);
2790    
2791    Write a line of data to a tab-delimited file. The specified field values will be
2792    output in tab-separated form, with a trailing new-line.
2793    
2794    =over 4
2795    
2796    =item handle
2797    
2798    Output file handle.
2799    
2800    =item fields
2801    
2802    List of field values.
2803    
2804    =item eol (optional)
2805    
2806    End-of-line character (default is "\n").
2807    
2808    =back
2809    
2810    =cut
2811    
2812    sub PutLine {
2813        # Get the parameters.
2814        my ($handle, $fields, $eol) = @_;
2815        # Write the data.
2816        print $handle join("\t", @{$fields}) . ($eol || "\n");
2817    }
2818    
2819    
2820    =head3 PrintLine
2821    
2822        Tracer::PrintLine($line);
2823    
2824    Print a line of text with a trailing new-line.
2825    
2826    =over 4
2827    
2828    =item line
2829    
2830    Line of text to print.
2831    
2832    =back
2833    
2834    =cut
2835    
2836    sub PrintLine {
2837        # Get the parameters.
2838        my ($line) = @_;
2839        # Print the line.
2840        print "$line\n";
2841    }
2842    
2843    
2844    =head2 Other Useful Methods
2845    
2846    =head3 IDHASH
2847    
2848        my $hash = SHTargetSearch::IDHASH(@keys);
2849    
2850    This is a dinky little method that converts a list of values to a reference
2851    to hash of values to labels. The values and labels are the same.
2852    
2853    =cut
2854    
2855    sub IDHASH {
2856        my %retVal = map { $_ => $_ } @_;
2857        return \%retVal;
2858    }
2859    
2860    =head3 Pluralize
2861    
2862        my $plural = Tracer::Pluralize($word);
2863    
2864    This is a very simple pluralization utility. It adds an C<s> at the end
2865    of the input word unless it already ends in an C<s>, in which case it
2866    adds C<es>.
2867    
2868  =over 4  =over 4
2869    
2870  =item optionTable  =item word
2871    
2872  Table of default options.  Singular word to pluralize.
2873    
2874    =item RETURN
2875    
2876    Returns the probable plural form of the word.
2877    
2878    =back
2879    
2880    =cut
2881    
2882    sub Pluralize {
2883        # Get the parameters.
2884        my ($word) = @_;
2885        # Declare the return variable.
2886        my $retVal;
2887        if ($word =~ /s$/) {
2888            $retVal = $word . 'es';
2889        } else {
2890            $retVal = $word . 's';
2891        }
2892        # Return the result.
2893        return $retVal;
2894    }
2895    
2896    =head3 Numeric
2897    
2898        my $okFlag = Tracer::Numeric($string);
2899    
2900    Return the value of the specified string if it is numeric, or an undefined value
2901    if it is not numeric.
2902    
2903    =over 4
2904    
2905    =item string
2906    
2907    String to check.
2908    
2909    =item RETURN
2910    
2911    Returns the numeric value of the string if successful, or C<undef> if the string
2912    is not numeric.
2913    
2914    =back
2915    
2916    =cut
2917    
2918    sub Numeric {
2919        # Get the parameters.
2920        my ($string) = @_;
2921        # We'll put the value in here if we succeed.
2922        my $retVal;
2923        # Get a working copy of the string.
2924        my $copy = $string;
2925        # Trim leading and trailing spaces.
2926        $copy =~ s/^\s+//;
2927        $copy =~ s/\s+$//;
2928        # Check the result.
2929        if ($copy =~ /^[+-]?\d+$/) {
2930            $retVal = $copy;
2931        } elsif ($copy =~ /^([+-]\d+|\d*)[eE][+-]?\d+$/) {
2932            $retVal = $copy;
2933        } elsif ($copy =~ /^([+-]\d+|\d*)\.\d*([eE][+-]?\d+)?$/) {
2934            $retVal = $copy;
2935        }
2936        # Return the result.
2937        return $retVal;
2938    }
2939    
2940    
2941    =head3 ParseParm
2942    
2943        my $listValue = Tracer::ParseParm($string);
2944    
2945    Convert a parameter into a list reference. If the parameter is undefined,
2946    an undefined value will be returned. Otherwise, it will be parsed as a
2947    comma-separated list of values.
2948    
2949    =over 4
2950    
2951    =item string
2952    
2953    Incoming string.
2954    
2955    =item RETURN
2956    
2957    Returns a reference to a list of values, or C<undef> if the incoming value
2958    was undefined.
2959    
2960    =back
2961    
2962    =cut
2963    
2964    sub ParseParm {
2965        # Get the parameters.
2966        my ($string) = @_;
2967        # Declare the return variable.
2968        my $retVal;
2969        # Check for data.
2970        if (defined $string) {
2971            # We have some, so split it into a list.
2972            $retVal = [ split /\s*,\s*/, $string];
2973        }
2974        # Return the result.
2975        return $retVal;
2976    }
2977    
2978    =head3 Now
2979    
2980        my $string = Tracer::Now();
2981    
2982    Return a displayable time stamp containing the local time. Whatever format this
2983    method produces must be parseable by L</ParseDate>.
2984    
2985    =cut
2986    
2987    sub Now {
2988        return DisplayTime(time);
2989    }
2990    
2991    =head3 DisplayTime
2992    
2993        my $string = Tracer::DisplayTime($time);
2994    
2995    Convert a time value to a displayable time stamp. Whatever format this
2996    method produces must be parseable by L</ParseDate>.
2997    
2998    =over 4
2999    
3000    =item time
3001    
3002    Time to display, in seconds since the epoch, or C<undef> if the time is unknown.
3003    
3004    =item RETURN
3005    
3006    Returns a displayable time, or C<(n/a)> if the incoming time is undefined.
3007    
3008    =back
3009    
3010    =cut
3011    
3012    sub DisplayTime {
3013        my ($time) = @_;
3014        my $retVal = "(n/a)";
3015        if (defined $time) {
3016            my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime($time);
3017            $retVal = _p2($mon+1) . "/" . _p2($mday) . "/" . ($year + 1900) . " " .
3018                      _p2($hour) . ":" . _p2($min) . ":" . _p2($sec);
3019        }
3020        return $retVal;
3021    }
3022    
3023    # Pad a number to 2 digits.
3024    sub _p2 {
3025        my ($value) = @_;
3026        $value = "0$value" if ($value < 10);
3027        return $value;
3028    }
3029    
3030    =head3 Escape
3031    
3032        my $codedString = Tracer::Escape($realString);
3033    
3034    Escape a string for use in a command. Tabs will be replaced by C<\t>, new-lines
3035    replaced by C<\n>, carriage returns will be deleted, and backslashes will be doubled. The
3036    result is to reverse the effect of L</UnEscape>.
3037    
3038    =over 4
3039    
3040    =item realString
3041    
3042    String to escape.
3043    
3044    =item RETURN
3045    
3046    Escaped equivalent of the real string.
3047    
3048    =back
3049    
3050    =cut
3051    
3052    sub Escape {
3053        # Get the parameter.
3054        my ($realString) = @_;
3055        # Initialize the return variable.
3056        my $retVal = "";
3057        # Loop through the parameter string, looking for sequences to escape.
3058        while (length $realString > 0) {
3059            # Look for the first sequence to escape.
3060            if ($realString =~ /^(.*?)([\n\t\r\\])/) {
3061                # Here we found it. The text preceding the sequence is in $1. The sequence
3062                # itself is in $2. First, move the clear text to the return variable.
3063                $retVal .= $1;
3064                # Strip the processed section off the real string.
3065                $realString = substr $realString, (length $2) + (length $1);
3066                # Get the matched character.
3067                my $char = $2;
3068                # If we have a CR, we are done.
3069                if ($char ne "\r") {
3070                    # It's not a CR, so encode the escape sequence.
3071                    $char =~ tr/\t\n/tn/;
3072                    $retVal .= "\\" . $char;
3073                }
3074            } else {
3075                # Here there are no more escape sequences. The rest of the string is
3076                # transferred unmodified.
3077                $retVal .= $realString;
3078                $realString = "";
3079            }
3080        }
3081        # Return the result.
3082        return $retVal;
3083    }
3084    
3085    =head3 UnEscape
3086    
3087        my $realString = Tracer::UnEscape($codedString);
3088    
3089    Replace escape sequences with their actual equivalents. C<\t> will be replaced by
3090    a tab, C<\n> by a new-line character, and C<\\> by a backslash. C<\r> codes will
3091    be deleted.
3092    
3093    =over 4
3094    
3095    =item codedString
3096    
3097    String to un-escape.
3098    
3099    =item RETURN
3100    
3101    Returns a copy of the original string with the escape sequences converted to their actual
3102    values.
3103    
3104    =back
3105    
3106    =cut
3107    
3108    sub UnEscape {
3109        # Get the parameter.
3110        my ($codedString) = @_;
3111        # Initialize the return variable.
3112        my $retVal = "";
3113        # Only proceed if the incoming string is nonempty.
3114        if (defined $codedString) {
3115            # Loop through the parameter string, looking for escape sequences. We can't do
3116            # translating because it causes problems with the escaped slash. ("\\t" becomes
3117            # "\<tab>" no matter what we do.)
3118            while (length $codedString > 0) {
3119                # Look for the first escape sequence.
3120                if ($codedString =~ /^(.*?)\\(\\|n|t|r)/) {
3121                    # Here we found it. The text preceding the sequence is in $1. The sequence
3122                    # itself is in $2. First, move the clear text to the return variable.
3123                    $retVal .= $1;
3124                    $codedString = substr $codedString, (2 + length $1);
3125                    # Get the escape value.
3126                    my $char = $2;
3127                    # If we have a "\r", we are done.
3128                    if ($char ne 'r') {
3129                        # Here it's not an 'r', so we convert it.
3130                        $char =~ tr/\\tn/\\\t\n/;
3131                        $retVal .= $char;
3132                    }
3133                } else {
3134                    # Here there are no more escape sequences. The rest of the string is
3135                    # transferred unmodified.
3136                    $retVal .= $codedString;
3137                    $codedString = "";
3138                }
3139            }
3140        }
3141        # Return the result.
3142        return $retVal;
3143    }
3144    
3145    =head3 Percent
3146    
3147        my $percent = Tracer::Percent($number, $base);
3148    
3149    Returns the percent of the base represented by the given number. If the base
3150    is zero, returns zero.
3151    
3152    =over 4
3153    
3154    =item number
3155    
3156    Percent numerator.
3157    
3158    =item base
3159    
3160    Percent base.
3161    
3162    =item RETURN
3163    
3164    Returns the percentage of the base represented by the numerator.
3165    
3166    =back
3167    
3168    =cut
3169    
3170    sub Percent {
3171        # Get the parameters.
3172        my ($number, $base) = @_;
3173        # Declare the return variable.
3174        my $retVal = 0;
3175        # Compute the percent.
3176        if ($base != 0) {
3177            $retVal = $number * 100 / $base;
3178        }
3179        # Return the result.
3180        return $retVal;
3181    }
3182    
3183    =head3 In
3184    
3185        my $flag = Tracer::In($value, $min, $max);
3186    
3187    Return TRUE if the value is between the minimum and the maximum, else FALSE.
3188    
3189    =cut
3190    
3191    sub In {
3192        return ($_[0] <= $_[2] && $_[0] >= $_[1]);
3193    }
3194    
3195    
3196    =head3 Constrain
3197    
3198        my $constrained = Constrain($value, $min, $max);
3199    
3200    Modify a numeric value to bring it to a point in between a maximum and a minimum.
3201    
3202    =over 4
3203    
3204    =item value
3205    
3206    Value to constrain.
3207    
3208    =item min (optional)
3209    
3210    Minimum permissible value. If this parameter is undefined, no minimum constraint will be applied.
3211    
3212    =item max (optional)
3213    
3214    Maximum permissible value. If this parameter is undefined, no maximum constraint will be applied.
3215    
3216    =item RETURN
3217    
3218    Returns the incoming value, constrained according to the other parameters.
3219    
3220    =back
3221    
3222    =cut
3223    
3224    sub Constrain {
3225        # Get the parameters.
3226        my ($value, $min, $max) = @_;
3227        # Declare the return variable.
3228        my $retVal = $value;
3229        # Apply the minimum constraint.
3230        if (defined $min && $retVal < $min) {
3231            $retVal = $min;
3232        }
3233        # Apply the maximum constraint.
3234        if (defined $max && $retVal > $max) {
3235            $retVal = $max;
3236        }
3237        # Return the result.
3238        return $retVal;
3239    }
3240    
3241    =head3 Min
3242    
3243        my $min = Min($value1, $value2, ... $valueN);
3244    
3245    Return the minimum argument. The arguments are treated as numbers.
3246    
3247    =over 4
3248    
3249  =item inputList  =item $value1, $value2, ... $valueN
3250    
3251  List of words on the command line.  List of numbers to compare.
3252    
3253  =item RETURN  =item RETURN
3254    
3255  Returns a reference to the option table and a list of the positional arguments.  Returns the lowest number in the list.
3256    
3257  =back  =back
3258    
3259  =cut  =cut
3260    
3261  sub ParseCommand {  sub Min {
3262          # Get the parameters.      # Get the parameters. Note that we prime the return value with the first parameter.
3263          my ($optionTable, @inputList) = @_;      my ($retVal, @values) = @_;
3264          # Process any options in the input list.      # Loop through the remaining parameters, looking for the lowest.
3265          my %overrides = ();      for my $value (@values) {
3266          while ((@inputList > 0) && ($inputList[0] =~ /^-/)) {          if ($value < $retVal) {
3267                  # Get the current option.              $retVal = $value;
                 my $arg = shift @inputList;  
                 # Pull out the option name.  
                 $arg =~ /^-([^=]*)/g;  
                 my $name = $1;  
                 # Check for an option value.  
                 if ($arg =~ /\G=(.*)$/g) {  
                         # Here we have a value for the option.  
                         $overrides{$name} = UnEscape($1);  
                 } else {  
                         # Here there is no value, so we use 1.  
                         $overrides{$name} = 1;  
                 }  
3268          }          }
         # Merge the options into the defaults.  
         GetOptions($optionTable, \%overrides);  
         # Translate the remaining parameters.  
         my @retVal = ();  
         for my $inputParm (@inputList) {  
                 push @retVal, UnEscape($inputParm);  
3269          }          }
3270          # Return the results.      # Return the minimum found.
3271          return ($optionTable, @retVal);      return $retVal;
3272  }  }
3273    
3274  =head3 Escape  =head3 Max
3275    
3276  C<< my $codedString = Tracer::Escape($realString); >>      my $max = Max($value1, $value2, ... $valueN);
3277    
3278  Escape a string for use in a command length. Spaces will be replaced by C<\b>,  Return the maximum argument. The arguments are treated as numbers.
 tabs replaced by C<\t>, new-lines replaced by C<\n>, and backslashes will be  
 doubled. The effect is to exactly reverse the effect of L</UnEscape>.  
3279    
3280  =over 4  =over 4
3281    
3282  =item realString  =item $value1, $value2, ... $valueN
3283    
3284  String to escape.  List of numbers to compare.
3285    
3286  =item RETURN  =item RETURN
3287    
3288  Escaped equivalent of the real string.  Returns the highest number in the list.
3289    
3290  =back  =back
3291    
3292  =cut  =cut
3293    
3294  sub Escape {  sub Max {
3295          # Get the parameter.      # Get the parameters. Note that we prime the return value with the first parameter.
3296          my ($realString) = @_;      my ($retVal, @values) = @_;
3297          # Initialize the return variable.      # Loop through the remaining parameters, looking for the highest.
3298          my $retVal = "";      for my $value (@values) {
3299          # Loop through the parameter string, looking for sequences to escape.          if ($value > $retVal) {
3300          while (length $realString > 0) {              $retVal = $value;
                 # Look for the first sequence to escape.  
                 if ($realString =~ /^(.*?)([ \n\t\\])/) {  
                         # Here we found it. The text preceding the sequence is in $1. The sequence  
                         # itself is in $2. First, move the clear text to the return variable.  
                         $retVal .= $1;  
                         $realString = substr $realString, (length $2 + length $1);  
                         # Encode the escape sequence.  
                         my $char = $2;  
                         $char =~ tr/ \t\n/btn/;  
                         $retVal .= "\\" . $char;  
                 } else {  
                         # Here there are no more escape sequences. The rest of the string is  
                         # transferred unmodified.  
                         $retVal .= $realString;  
                         $realString = "";  
3301                  }                  }
3302          }          }
3303          # Return the result.      # Return the maximum found.
3304          return $retVal;          return $retVal;
3305  }  }
3306    
3307  =head3 UnEscape  =head3 Strip
3308    
3309  C<< my $realString = Tracer::UnEscape($codedString); >>      my $string = Tracer::Strip($line);
3310    
3311  Replace escape sequences with their actual equivalents. C<\b> will be replaced by a space,  Strip all line terminators off a string. This is necessary when dealing with files
3312  C<\t> by a tab, C<\n> by a new-line character, and C<\\> by a back-slash.  that may have been transferred back and forth several times among different
3313    operating environments.
3314    
3315  =over 4  =over 4
3316    
3317  =item codedString  =item line
3318    
3319  String to un-escape.  Line of text to be stripped.
3320    
3321  =item RETURN  =item RETURN
3322    
3323  Returns a copy of the original string with the escape sequences converted to their actual  The same line of text with all the line-ending characters chopped from the end.
 values.  
3324    
3325  =back  =back
3326    
3327  =cut  =cut
3328    
3329  sub UnEscape {  sub Strip {
3330          # Get the parameter.      # Get a copy of the parameter string.
3331          my ($codedString) = @_;      my ($string) = @_;
3332          # Initialize the return variable.      my $retVal = (defined $string ? $string : "");
3333          my $retVal = "";      # Strip the line terminator characters.
3334          # Only proceed if the incoming string is nonempty.      $retVal =~ s/(\r|\n)+$//g;
         if (defined $codedString) {  
                 # Loop through the parameter string, looking for escape sequences. We can't do  
                 # translating because it causes problems with the escaped slash. ("\\b" becomes  
                 # "\ " no matter what we do.)  
                 while (length $codedString > 0) {  
                         # Look for the first escape sequence.  
                         if ($codedString =~ /^(.*?)\\(\\|b|n|t)/) {  
                                 # Here we found it. The text preceding the sequence is in $1. The sequence  
                                 # itself is in $2. First, move the clear text to the return variable.  
                                 $retVal .= $1;  
                                 $codedString = substr $codedString, (2 + length $1);  
                                 # Decode the escape sequence.  
                                 my $char = $2;  
                                 $char =~ tr/\\btn/\\ \t\n/;  
                                 $retVal .= $char;  
                         } else {  
                                 # Here there are no more escape sequences. The rest of the string is  
                                 # transferred unmodified.  
                                 $retVal .= $codedString;  
                                 $codedString = "";  
                         }  
                 }  
         }  
3335          # Return the result.          # Return the result.
3336          return $retVal;          return $retVal;
3337  }  }
3338    
3339  =head3 ParseRecord  =head3 Trim
3340    
3341  C<< my @fields = Tracer::ParseRecord($line); >>      my $string = Tracer::Trim($line);
3342    
3343  Parse a tab-delimited data line. The data line is split into field values. Embedded tab  Trim all spaces from the beginning and ending of a string.
 and new-line characters in the data line must be represented as C<\t> and C<\n>, respectively.  
 These will automatically be converted.  
3344    
3345  =over 4  =over 4
3346    
3347  =item line  =item line
3348    
3349  Line of data containing the tab-delimited fields.  Line of text to be trimmed.
3350    
3351  =item RETURN  =item RETURN
3352    
3353  Returns a list of the fields found in the data line.  The same line of text with all whitespace chopped off either end.
3354    
3355  =back  =back
3356    
3357  =cut  =cut
3358    
3359  sub ParseRecord {  sub Trim {
3360          # Get the parameter.      # Get a copy of the parameter string.
3361          my ($line) = @_;      my ($string) = @_;
3362          # Remove the trailing new-line, if any.      my $retVal = (defined $string ? $string : "");
3363          chomp $line;      # Strip the front spaces.
3364          # Split the line read into pieces using the tab character.      $retVal =~ s/^\s+//;
3365          my @retVal = split /\t/, $line;      # Strip the back spaces.
3366          # Trim and fix the escapes in each piece.      $retVal =~ s/\s+$//;
         for my $value (@retVal) {  
                 # Trim leading whitespace.  
                 $value =~ s/^\s+//;  
                 # Trim trailing whitespace.  
                 $value =~ s/\s+$//;  
                 # Delete the carriage returns.  
                 $value =~ s/\r//g;  
                 # Convert the escapes into their real values.  
                 $value =~ s/\\t/"\t"/ge;  
                 $value =~ s/\\n/"\n"/ge;  
         }  
3367          # Return the result.          # Return the result.
3368          return @retVal;      return $retVal;
3369  }  }
3370    
3371  =head3 Merge  =head3 Pad
3372    
3373  C<< my @mergedList = Tracer::Merge(@inputList); >>      my $paddedString = Tracer::Pad($string, $len, $left, $padChar);
3374    
3375  Sort a list of strings and remove duplicates.  Pad a string to a specified length. The pad character will be a
3376    space, and the padding will be on the right side unless specified
3377    in the third parameter.
3378    
3379  =over 4  =over 4
3380    
3381  =item inputList  =item string
3382    
3383  List of scalars to sort and merge.  String to be padded.
3384    
3385    =item len
3386    
3387    Desired length of the padded string.
3388    
3389    =item left (optional)
3390    
3391    TRUE if the string is to be left-padded; otherwise it will be padded on the right.
3392    
3393    =item padChar (optional)
3394    
3395    Character to use for padding. The default is a space.
3396    
3397  =item RETURN  =item RETURN
3398    
3399  Returns a list containing the same elements sorted in ascending order with duplicates  Returns a copy of the original string with the pad character added to the
3400  removed.  specified end so that it achieves the desired length.
3401    
3402  =back  =back
3403    
3404  =cut  =cut
3405    
3406  sub Merge {  sub Pad {
3407          # Get the input list in sort order.      # Get the parameters.
3408          my @inputList = sort @_;      my ($string, $len, $left, $padChar) = @_;
3409          # Only proceed if the list has at least two elements.      # Compute the padding character.
3410          if (@inputList > 1) {      if (! defined $padChar) {
3411                  # Now we want to move through the list splicing out duplicates.          $padChar = " ";
                 my $i = 0;  
                 while ($i < @inputList) {  
                         # Get the current entry.  
                         my $thisEntry = $inputList[$i];  
                         # Find out how many elements duplicate the current entry.  
                         my $j = $i + 1;  
                         my $dup1 = $i + 1;  
                         while ($j < @inputList && $inputList[$j] eq $thisEntry) { $j++; };  
                         # If the number is nonzero, splice out the duplicates found.  
                         if ($j > $dup1) {  
                                 splice @inputList, $dup1, $j - $dup1;  
3412                          }                          }
3413                          # Now the element at position $dup1 is different from the element before it      # Compute the number of spaces needed.
3414                          # at position $i. We push $i forward one position and start again.      my $needed = $len - length $string;
3415                          $i++;      # Copy the string into the return variable.
3416        my $retVal = $string;
3417        # Only proceed if padding is needed.
3418        if ($needed > 0) {
3419            # Create the pad string.
3420            my $pad = $padChar x $needed;
3421            # Affix it to the return value.
3422            if ($left) {
3423                $retVal = $pad . $retVal;
3424            } else {
3425                $retVal .= $pad;
3426                  }                  }
3427          }          }
3428          # Return the merged list.      # Return the result.
3429          return @inputList;      return $retVal;
3430    }
3431    
3432    =head3 EOF
3433    
3434    This is a constant that is lexically greater than any useful string.
3435    
3436    =cut
3437    
3438    sub EOF {
3439        return "\xFF\xFF\xFF\xFF\xFF";
3440    }
3441    
3442    =head3 TICK
3443    
3444        my @results = TICK($commandString);
3445    
3446    Perform a back-tick operation on a command. If this is a Windows environment, any leading
3447    dot-slash (C<./> will be removed. So, for example, if you were doing
3448    
3449        `./protein.cgi`
3450    
3451    from inside a CGI script, it would work fine in Unix, but would issue an error message
3452    in Windows complaining that C<'.'> is not a valid command. If instead you code
3453    
3454        TICK("./protein.cgi")
3455    
3456    it will work correctly in both environments.
3457    
3458    =over 4
3459    
3460    =item commandString
3461    
3462    The command string to pass to the system.
3463    
3464    =item RETURN
3465    
3466    Returns the standard output from the specified command, as a list.
3467    
3468    =back
3469    
3470    =cut
3471    #: Return Type @;
3472    sub TICK {
3473        # Get the parameters.
3474        my ($commandString) = @_;
3475        # Chop off the dot-slash if this is Windows.
3476        if ($FIG_Config::win_mode) {
3477            $commandString =~ s!^\./!!;
3478        }
3479        # Activate the command and return the result.
3480        return `$commandString`;
3481    }
3482    
3483    
3484    =head3 CommaFormat
3485    
3486        my $formatted = Tracer::CommaFormat($number);
3487    
3488    Insert commas into a number.
3489    
3490    =over 4
3491    
3492    =item number
3493    
3494    A sequence of digits.
3495    
3496    =item RETURN
3497    
3498    Returns the same digits with commas strategically inserted.
3499    
3500    =back
3501    
3502    =cut
3503    
3504    sub CommaFormat {
3505        # Get the parameters.
3506        my ($number) = @_;
3507        # Pad the length up to a multiple of three.
3508        my $padded = "$number";
3509        $padded = " " . $padded while length($padded) % 3 != 0;
3510        # This is a fancy PERL trick. The parentheses in the SPLIT pattern
3511        # cause the delimiters to be included in the output stream. The
3512        # GREP removes the empty strings in between the delimiters.
3513        my $retVal = join(",", grep { $_ ne '' } split(/(...)/, $padded));
3514        # Clean out the spaces.
3515        $retVal =~ s/ //g;
3516        # Return the result.
3517        return $retVal;
3518  }  }
3519    
 =head3 GetFile  
3520    
3521  C<< my @fileContents = Tracer::GetFile($fileName); >>  =head3 CompareLists
3522    
3523        my ($inserted, $deleted) = Tracer::CompareLists(\@newList, \@oldList, $keyIndex);
3524    
3525  Return the entire contents of a file.  Compare two lists of tuples, and return a hash analyzing the differences. The lists
3526    are presumed to be sorted alphabetically by the value in the $keyIndex column.
3527    The return value contains a list of items that are only in the new list
3528    (inserted) and only in the old list (deleted).
3529    
3530  =over 4  =over 4
3531    
3532  =item fileName  =item newList
3533    
3534  Name of the file to read.  Reference to a list of new tuples.
3535    
3536    =item oldList
3537    
3538    Reference to a list of old tuples.
3539    
3540    =item keyIndex (optional)
3541    
3542    Index into each tuple of its key field. The default is 0.
3543    
3544  =item RETURN  =item RETURN
3545    
3546  In a list context, returns the entire file as a list with the line terminators removed.  Returns a 2-tuple consisting of a reference to the list of items that are only in the new
3547  In a scalar context, returns the entire file as a string.  list (inserted) followed by a reference to the list of items that are only in the old
3548    list (deleted).
3549    
3550  =back  =back
3551    
3552  =cut  =cut
3553    
3554  sub GetFile {  sub CompareLists {
3555          # Get the parameters.          # Get the parameters.
3556          my ($fileName) = @_;      my ($newList, $oldList, $keyIndex) = @_;
3557          # Declare the return variable.      if (! defined $keyIndex) {
3558          my @retVal = ();          $keyIndex = 0;
3559          # Open the file for input.      }
3560          my $ok = open INPUTFILE, "<$fileName";      # Declare the return variables.
3561          if (!$ok) {      my ($inserted, $deleted) = ([], []);
3562                  # If we had an error, trace it. We will automatically return a null value.      # Loop through the two lists simultaneously.
3563                  Trace("Could not open \"$fileName\" for input.") if T(0);      my ($newI, $oldI) = (0, 0);
3564        my ($newN, $oldN) = (scalar @{$newList}, scalar @{$oldList});
3565        while ($newI < $newN || $oldI < $oldN) {
3566            # Get the current object in each list. Note that if one
3567            # of the lists is past the end, we'll get undef.
3568            my $newItem = $newList->[$newI];
3569            my $oldItem = $oldList->[$oldI];
3570         &nb